Cytopathology of Infectious Diseases

Cytopathology of Infectious Diseases
ESSENTIALS IN CYTOPATHOLOGY
Dorothy L. Rosenthal, MD, FIAC, Series Editor
Editorial Board
Syed Z. Ali, MD
Douglas P. Clark, MD
Yener S. Erozan, MD
For further volumes:

http://www.springer.com/series/6996
Liron Pantanowitz, MD, MIAC
Pam Michelow, MBBCh, MSc (Med Sci)
Walid E. Khalbuss, MD, PhD, FIAC
Cytopathology
of Infectious Diseases
Including Chapters 2 & 14 Co-authored by:
Tanvier Omar, MB BCH, FC Path (S.A.)
Chapters 3, 9, 10 & 13 Co-authored by:
Sara E. Monaco, MD
Chapter 4 Co-authored by:
Gladwyn Leiman, MBBCh, FIAC, FRCPath
Lynne S. Garcia, MS, CLS, FAAM
R. Marshall Austin, MD, PhD
Rodolfo Laucirica, MD
Robert M. Najarian, MD
Helen H. Wang, MD, PhD
Anil V. Parwani, MD, PhD
and Chapter 15 Co-authored by:
Robert A. Goulart, MD
Rafael Martínez-Girón, MD, PhD
Liron Pantanowitz, MD, MIAC Pam Michelow, MBBCh,
Department of Pathology MSc (Med Sci)
University of Pittsburgh Department of Anatomical
Medical Center Pathology, University of the
Pittsburgh, PA 15232, USA Witwatersrand & National Health
pantanowitzl@upmc.edu Laboratory Service
Johannesburg 2000, South Africa
Walid E. Khalbuss, MD, PhD, FIAC pamela.michelow@nhls.ac.za
Department of Pathology
University of Pittsburgh
Medical Center
Pittsburgh, PA 15232, USA
khalbussw2@upmc.edu
ISSN 1574-9053 e-ISSN 1574-9061

ISBN 978-1-4614-0241-1 e-ISBN 978-1-4614-0242-8
DOI 10.1007/978-1-4614-0242-8
Springer New York Dordrecht Heidelberg London
Library of Congress Control Number: 2011932800
© Springer Science+Business Media, LLC 2011

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Printed on acid-free paper
Springer is part of Springer Science+Business Media (www.springer.com)

This book is dedicated to my wife Heidi and children
Joshua and Maya.
To my husband Alan and children Gina, Matt, and Aaron.

Pam Michelow, MBBCh, MSc (Med Sci)
To my family, mentors, trainees, and friends

for their encouragement and support.
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Foreword
Although it is long overdue, finally there is a textbook developed

entirely to the cytology diagnosis of infectious diseases, despite
the fact that since the early twentieth century there were a number
of reports documenting the utility of cytology examination. Greig
and Gray were the first to describe fine needle aspiration (FNA)
cytology for the diagnosis of infectious disease in their 1904 report
of biopsies of lymph nodes from fifteen patients with sleeping sick-
ness. Proscher used FNA cytology of lymph nodes for the diagnosis
of spirochetal infections in 1907, along with other investigators
reporting the use of FNA cytology for the diagnosis of filariasis,
bubonic plague, and spirochetes in secondary syphilis. In 1921,
Guthrie reported FNA biopsy of lymph nodes using air-dried,
Romanowsky-stained smears in cases of syphilis, tuberculosis,
simple adenitis, and trypanosomiasis. Guthrie also reported the use
of special stains for organisms including Ziehl-Neelsen stain for
acid fast bacilli, along with dark field examination for spirochetes
and reported bacteria such as streptococci and staphylococci in
lymph node aspirates.
Despite these early successes in the use of cytology for the
diagnosis of infectious disease, beginning in 1925 at Memorial
Hospital in New York, FNA began to be used mainly to diagnose
neoplastic conditions, although infectious diseases such as tuber-
culosis, syphilis, and actinomyces were occasionally encountered.
However, the dynamic explosion of FNA cytology for the diag-
nosis of neoplastic disease initially took place in Scandinavia by
clinician/cytopathologists. Following their seminal contributions,
vii
viii Foreword
FNA cytology had a rebirth in the USA due to the contributions of

a number of outstanding cytopathologists.
It has been over 20 years since I have had the opportunity to
publish a text on FNA of infectious and inflammatory diseases and
other nonneoplastic disorders. Since that time, there has been a
renewed interest in the cytologic diagnosis of infectious disease
coinciding with increased incidence of common and unusual infec-
tions due to the AIDS epidemic, expansion of organ transplanta-
tion, and aggressive treatment of neoplastic diseases resulting in an
increasing population of immunocompromised patients.
Now stepping forward to fill the void are Pantanowitz, Michelow
and Khalbuss with their associates, who have written the first text
devoted entirely to the cytopathology of infectious diseases. The
authors’ format is user friendly, presenting in a very concise for-
mat the clinical, cytomorphologic features, differential diagnosis,
pitfalls, and ancillary studies of a wide range of infectious diseases
that can be appreciated in cytology specimens. I believe the reader,
whether in training or a practicing pathologist, will benefit from
the authors’ extensive experience in the cytologic diagnosis of
infectious agents that can be encountered both in developing and
industrial nations. It is with great pleasure to have this opportu-
nity to recognize the outstanding cytopathologists who share their
extensive experience in this much-needed cytology monograph.
Jan F. Silverman, MD
Pittsburgh, PA, USA
Series Preface
The subspeciality of cytopathology is over 60 years old and has

become an established and reliable discipline in medicine. As
expected, cytopathology literature has expanded in a remarkably
short period of time, from a few textbooks prior to the 1980s to a
currently substantial library of texts and journals devoted exclu-
sively to cytomorphology. The Essentials in Cytopathology Series
does not presume to replace any of the distinguished textbooks in
cytopathology. Instead, the Series has published generously illus-
trated and user-friendly guides for both pathologists and clinicians.
The Series has met with gratifying success, and we now present
volume 10, with more than five volumes scheduled to come.
Built on the amazing success of The Bethesda System for
Reporting Cervical Cytology, now in its second edition, the Series
has utilized a similar format, including minimal text, tabular criteria,
and superb illustrations based on real-life specimens. Essentials in
Cytopathology has, at times, deviated from the classic organiza-
tion of pathology texts. The logic of decision trees, elimination of
unlikely choices, and narrowing of differential diagnosis via a prag-
matic approach based on morphologic criteria are some of the strat-
egies used to illustrate principles and practice in cytopathology.
Most of the authors for Essentials in Cytopathology are faculty
members in The Johns Hopkins University School of Medicine,
Department of Pathology, Division of Cytopathology. They bring
to each volume the legacy of John K. Frost and the collective
experience of a preeminent cytopathology service. The archives
at Hopkins are meticulously catalogued and form the framework
for text and illustrations. Authors from other institutions have been
selected on the basis of their national reputations, experience,
ix
x Series Preface
and enthusiasm for cytopathology. They bring to the series,

complementary viewpoints and enlarge the scope of materials
contained in the photographs.
The editor and the authors are indebted to our students, past and
future, who challenge and motivate us to become the best that we
possibly can be. We share that experience with you through these
pages, and hope that you will learn from them as we have from
those who have come before us. We would be remiss if we did not
pay tribute to our professional colleagues, the cytotechnologists,
and preparatory technicians, who lovingly care for the specimens that
our clinical colleagues send to us. We are also grateful to Springer
and its production staff for their enthusiasm, responsiveness, and
patience.
And finally, we cannot emphasize enough throughout these vol-
umes the importance of collaboration with the patient care team.
Every specimen comes to us with questions begging answers.
Without input from the clinicians, complete patient history, results
of imaging studies, and other ancillary tests, we cannot perform
optimally. It is our responsibility to educate our clinicians about
their role in our interpretation, and for us to integrate as much
information as we can gather into our final diagnosis, even if the
answer at first seems obvious.
We hope you will find this Series useful and welcome your feed-
back as you place these handbooks by your microscopes and into
your book bags.
Dorothy L. Rosenthal
Baltimore, MD, USA
drosenthal@jhmi.edu
Contents
Foreword................................................................................. vii
Series Preface.......................................................................... ix
1 Introduction..................................................................... 1
2 Specimen Collection and Handling................................ 5
3 Host Reactions to Infection............................................. 13
4 Microbiology................................................................... 37
5 Gynecological Infections................................................ 85
6 Pulmonary Infections...................................................... 121
7 Gastrointestinal and Hepatobiliary Infections................ 161
8 Urinary Tract Infections.................................................. 183
9 Central Nervous System Infections................................ 205
10 Hematologic Infections................................................... 231
11 Breast, Skin, and Musculoskeletal Infections................. 257
12 Head and Neck Infections............................................... 279
13 Immunosuppressed Host................................................. 299
14 Ancillary Investigations.................................................. 321
15 Mimics and Contaminants.............................................. 351
Index....................................................................................... 379
xi
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Contributors
R. Marshall Austin, MD, PhD

Professor of Pathology, Department of Pathology,
Magee-Women’s Hospital of University of Pittsburgh
Medical Center, Pittsburgh, PA, USA
Lynne S. Garcia, MS, CLS, FAAM
Director, LSG and Associates, Santa Monica, CA, USA
Robert A. Goulart, MD
Director of Surgical Pathology and Hospital Pathology Services,
Associate Director of Cytopathology Services, New England
Pathology Associates, Mercy Medical Center of Sisters
of Providence Health System/Catholic Health East,
Springfield, MA, USA
Associate Professor of Pathology, Director of Cytology
and Cytopathology Fellowship Program,
Department of Pathology, University of Pittsburgh Medical
Center, Pittsburgh, PA, USA
Rodolfo Laucirica, MD
Associate Professor of Pathology and Immunology,
Director of the Cytopathology Fellowship Program,
Director of Cytology, Department of Pathology
and Immunology, Baylor College of Medicine,
Ben Taub General Hospital, Houston, TX, USA
xiii
xiv Contributors
Gladwyn Leiman, MBBCh, FIAC, FRCPath

Director of Cytopathology, Fletcher Allen Health Care,
Professor of Pathology, University of Vermont,
Burlington, VT, USA
Rafael Martínez-Girón, MD, PhD
Professor of Cytopathology, CF Anatomía Patológica y Citología,
Instituto de Piedras Blancas, Piedras Blancas, Asturias, Spain
Pam Michelow, MBBCh, MSc (Med Sci), MIAC
Chief Medical Officer, Faculty of Health Sciences,
Cytology Unit, Department of Anatomical Pathology,
University of the Witwatersrand and National Health
Laboratory Service, Johannesburg, Gauteng, South Africa
Sara E. Monaco, MD
Assistant Professor, Associate Director of Cytopathology
Fellowship, Department of Pathology, University of Pittsburgh
Medical Center, Pittsburgh, PA, USA
Robert M. Najarian, MD
Staff Pathologist and Consultant in Gastrointestinal
and Hepatobiliary Pathology, Department of Pathology,
Beth Israel Deaconess Medical Center/Harvard Medical School,
Boston, MA, USA
Tanvier Omar, MB BCH, FC Path (S.A.)
Principal Pathologist, Division of Cytopathology, Department
of Anatomical Pathology, National Health Laboratory Service
and University of Witwatersrand, Johannesburg, Gauteng,
South Africa
Associate Professor of Pathology and Biomedical Informatics,
Contributors xv
Anil V. Parwani, MD, PhD

Associate Professor of Pathology and Biomedical Informatics,
Helen H. Wang, MD, PhD
Director of Cytopathology, Associate Professor of Pathology,
Department of Pathology, Beth Israel Deaconess Medical Center/
Harvard Medical Center, Boston, MA, USA
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1
Introduction
Liron Pantanowitz1 and Pam Michelow2
1
Department of Pathology, University of Pittsburgh Medical Center,
5150 Centre Avenue, Suite 201, Pittsburgh, PA 15232, USA
2
Cytology Unit, Department of Anatomical Pathology, University of
the Witwatersrand and National Health Laboratory Service,
Johannesburg, Gauteng, South Africa
We believe that the examination of fluid removed from lymphatic glands

will prove to be a much more rapid and satisfactory method of diagnos-
ing early cases of sleeping sickness than the examination of blood. At
first the glands were excised, but this was soon found to be unneces-
sary, as it is easy to puncture a superficial gland with a hypodermic
syringe (Grieg 1904).
Cytopatholgy provides a rapid, inexpensive, simple, and effective

mechanism to diagnose and manage a wide range of infectious
diseases. A variety of ancillary techniques such as special stains,
immunocytochemistry, and molecular studies can be applied to
cytology samples, thereby increasing the specificity and sensitivity
of this procedure. As a result, cytology specimens can reliably pro-
vide timely and specific diagnoses as well as classify many micro-
organisms including viruses, bacteria, fungi, and parasites. While it
may be impossible to detect individual viruses by light microscopy,
the cytopathic changes they induce on infected cells are often read-
ily visible, even in routine preparations. The advantages of cytology
in the work-up of patients with infectious diseases include:
●● Specimen procurement: Rapid, minimally invasive, and cost-
effective procedure with minimal contamination. Specimens sub-
mitted for cytologic evaluation may be obtained via exfoliation,
abrasion, aspiration, or touch preparation.
L. Pantanowitz et al., Cytopathology of Infectious Diseases, 1

Essentials in Cytopathology 17, DOI 10.1007/978-1-4614-0242-8_1,
2 1. Introduction
●● Specimen triage: Rapid assessment with submission of additional

material for cell block preparation, cultures, special stains, flow
cytometry, and molecular tests.
●● Specimen diagnosis: Rapid diagnostic procedure to guide early
patient management, including timely implementation of infec-
tion control procedures if required. In many cases a diagno-
sis can be obtained sooner than microbiology testing or tissue
biopsy. Mycobacterial and fungal cultures, for example, often
take several weeks to yield an answer.
Cytology specimens can be obtained from clinics and outpa-
tient settings, hospitalized, and even critically ill or intraoperative
patients. The emergence of opportunistic infections in transplant
recipients and AIDS patients has increased the need for minimally
invasive rapid diagnostic methods. The resurgence of previously
rare infections is also largely due to the increasing incidence of
immunocompromised patients. Fine needle aspiration (FNA)
biopsy permits the evaluation of superficial and deep masses.
Cytologists can play a key role in the immediate interpretation of
material, rapidly identifying infectious cases at the patient’s bed-
side that may benefit from additional material and/or ancillary
studies. Consequently, cytology as an accepted modality to reli-
ably diagnose infectious disease has come a long way from one of
the first recorded instances in 1904 when FNA was employed to
diagnose trypanosomiasis.
Microorganisms are frequently encountered in cytology speci-
mens. The identification of these microorganisms based upon cyto-
morphologic appearance can on occasion be challenging and hence
require ancillary studies. For example, numerous collapsed pneu-
mocystis cysts may appear to be “budding,” while capsule deficient
cryptococcus may be mistaken for other microorganisms such as
histoplasmosis. Evaluation of the host response to organisms pro-
vides important clues to the diagnosis of infections. The potential to
render a false positive diagnosis of malignancy exists when inflam-
matory atypia and/or repair accompanies an infection. Conversely,
there is increased risk for a false negative diagnosis when neo-
plasms have a prominent inflammatory component or concomitant
infection. Endogenous structures and contaminants may also mimic
pathogens. There have been numerous texts describing the micro-
biology and pathology of microorganisms seen in tissue specimens.
Introduction 3
However, very few books deal with the cytomorphologic features

of these infectious diseases. Major changes in the screening, treat-
ment, and prevention (e.g., vaccination) of certain infections such
as human papillomavirus (HPV) have recently impacted the field
of cytopathology.
This book deals entirely with the cytopathology of infectious
diseases. This textbook covers the cytomorphology, differential
diagnoses, and pitfalls of common and uncommon infectious dis-
eases, and provides a practical approach to their diagnosis. Many
color images are included along with tables and simple diagrams
that serve as quick reference guides. The content also provides
advice on specimen procurement and handling, processing of mate-
rial in the cytology laboratory, and incorporates recent advances in
the field. With the advent of immunocytochemistry, in situ hybridi-
zation and advanced molecular studies, no longer are cytologists
limited to identifying pathogens using only morphological and limited
special stain characteristics.
Suggested Reading
Atkins KA, Powers CN. The cytopathology of infectious diseases. Adv
Anat Pathol. 2002;9:52–64.
Grieg EDW, Gray ACH. Note on the lymphatic glands in sleeping sickness.
Br Med J. 1904;1:1252.
Jannes G, De Vos D. A review of current and future molecular diag-
nostic tests for use in the microbiology laboratory. Methods Mol Biol.
2006;345:1–21.
Kradin RL, editor. Diagnostic pathology of infectious disease. Philadelphia:
Saunders Elsevier; 2010.
Lal A, Warren J, Bedrossian CW, Nayar R. The role of fine needle aspira-
tion in diagnosis of infectious disease. Lab Med. 2002;11:866–72.
Powers CN. Diagnosis of infectious diseases: a cytopathologist’s perspective.
Clin Microbiol Rev. 1998;11:341–65.
Silverman JF, Gay RM. Fine-needle aspiration and surgical pathol-
ogy of infectious lesions. morphologic features and the role of the
clinical microbiology laboratory for rapid diagnosis. Clin Lab Med.
1995;15:251–78.
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2
Specimen Collection
and Handling
Pam Michelow1, Tanvier Omar2, and Liron Pantanowitz3
1
University of the Witwatersrand and National Health
Laboratory Service, Johannesburg, Gauteng, South Africa
2
Division of Cytopathology, Department of Anatomical Pathology,
National Health Laboratory Service and University of Witwatersrand,
3
Cytology is often performed in the investigation of patients with

suspected infection. This is because cytology provides a safe, rapid,
and cost-effective means to diagnose many infections, allowing
correct management to be instituted. Moreover, cytology permits
appropriate ancillary investigations to be undertaken either at the
time of specimen procurement (e.g., triage of material for microbi-
ology culture) (Fig. 2.1) or after material is processed (e.g., special
stains for microorganisms using cell block sections). The use of
ancillary investigations (e.g., cell block preparation, special stains,
immunocytochemistry, molecular studies) in cytopathology is
covered in Chap. 14. Appropriate specimen collection and han-
dling are essential to the diagnosis of infectious diseases. Sample
collection for pathogens needs to be coordinated. This requires
effective communication with clinicians, radiologists, and micro-
biologists, particularly if an uncommon infectious process is sus-
pected. Universal precautions must be followed when handling
specimens.

6 2. Specimen Collection and Handling
Fig. 2.1. Aspirated material obtained by FNA can be submitted by the

cytologist for microbiology studies such as culture using suitable sterile
containers or tubes (orange capped examples shown), along with some
sterile saline (two pink sterile saline solution packs shown) or placed on
moistened filter paper. Bacteriostatic saline or formalin should not be used.
Drying of specimens during transport may compromise the recovery of
viable organisms. Alternatively, sterile culture media can be used at the time
of specimen collection to directly transfer specimens obtained by FNA.
●● Virology. Methods used to diagnose viral infections include

antigen detection, virus isolation, serology, and molecular tech-
niques. While antigen detection is rapid, there may be many
false positives and negatives. The primary method to diagnose
many viruses (except EBV, for example) is with viral isolation
in cell culture, but this can take weeks. Specimens submitted
to culture viral agents may require special transport medium,
although media designed for transporting bacteria are often
acceptable. Viral detection in culture is carried out by visual
examination of culture cells for viral cytopathic effect (CPE)
Specimen Collection and Handling 7
Table 2.1. Characteristic viral inclusions observed in culture.

Nuclear Cytoplasmic
Virus inclusions inclusions Syncytia
Herpes simplex virus Yes No Yes
Cytomegalovirus Yes Yes No
Influenza No No No
Respiratory syncytial virus No No Yes
Adenovirus Yes No No
Measles Yes Yes Yes
(Table 2.1). Serology (detection of circulating antibodies)

relies on demonstrating a rise in antibody titers in sequential
samples.
●● Bacteriology. Bacteria are diagnosed by direct examination
(Gram and acid-fast staining) and culture (aerobic and anerobic)
using specific culture media (Fig. 2.2). Specimens for anero-
bic culture should ideally be submitted in anerobic containers
and immediately transported to the laboratory. A specimen
submitted in an anerobic container can also be used for aerobic,
mycobacterial, and fungal cultures. Mycobacteria are cultured
on both solid (e.g., Lowenstein-Jensen and Middlebrook agars)
and broth (e.g., BACTEC system, Mycobacterium Growth
Indicator Tube or MGIT) media.
●● Mycology. Fungi can be identified using direct examination (e.g.,
calcofluor white fluorescent stain, India ink), antigen detection
(e.g., cryptococcal antigen), and fungal culture (e.g., Sabouraud
agar). Yeasts (unicellular with budding) form small bacterial-
like creamy colonies in culture, whereas molds (multicellular
with hyphae) make large fuzzy colonies.
●● Parasitology. Parasites are usually not cultured. They are usually
diagnosed on direct examination using both wet mounts and
stained slides (e.g., modified acid-fast stains for Cryptosporid-
ium, Cyclospora, and Isospora). Wet mounts are useful to
identify motile trophozoites and cysts (often with iodide added).
Serology is of limited use in parasitology.
Fig. 2.2. Cytologic specimens received in the microbiology laboratory

get plated under a culture hood (left) onto various media such as (top
right) MacConkey agar, (middle right) chocolate agar, and (bottom right)
blood agar. Most pathogens are able to grow on blood agar, which is used
to initially culture most specimens. Other culture media like MacConkey
agar provide a selective and differential medium for specific bacteria (e.g.,
Gram-negative bacilli).
Specimen Type
●● Pap test (smear) involves scraping of the cervix with a cervi-
cal brush, broom, or wooden/plastic spatula. For anal Pap tests
a small brush or cotton-tipped rod is inserted into the anus.
Rinsing the collection device or detaching and placing it in
a vial containing proprietary preservative fluid (liquid-based
cytology) permits material to be processed for ancillary studies
(e.g., DNA testing for HPV, gonorrhea, and Chlamydia) and for
infections that cannot be reliably identified morphologically.
Conventional smears can also be used for ancillary studies
(e.g., HPV tests), by scraping material off slides.
Specimen Type 9
●● Wet prep can be performed at the patient bedside to provide

immediate microscopic examination of vaginal specimens (swab
or secretions) for the presence of Trichomonas vaginalis, clue
cells, and yeast in a saline suspension (e.g., 2 mL 0.9% NaCl)
with/without potassium hydroxide (20% KOH with dimethyl-
sulfoxide).
●● Tzanck test is a scraping of an ulcer base to look for infected
cells with herpetic changes due to herpes simplex virus (HSV)
or varicella-zoster virus (VSV). As these are often prepared by
clinicians and received on prepared slides, they are subject to
air-drying artifact without residual material to perform immu-
nocytochemistry. Due largely to sampling issues, there is a high
rate of false-negative results even when the virus is present.
●● Scrapings, swabs, or impressions may be performed to diag-
nose oropharyngeal (e.g., Candida) as well as conjunctival and
corneal (e.g., Herpes simplex keratitis and trachoma) infections.
The technique for performing impression cytology of the ocular
surface is described in Chap. 12.
●● Washings, brushings, and lavage typically involve an invasive
procedure (e.g., bronchoscopy) with infusion and reaspiration of
sterile saline solution. Samples can be submitted for cytological
evaluation and culture.
●● Fluids from effusions and other anatomic sites (e.g., CSF, urine,
joints) can be shared for cytological evaluation and a variety
of microbiology tests (e.g., serology, culture. PCR). Cytologic
preparation techniques include cytocentrifuge (larger volumes),
cytospins (smaller volumes <5 mL), membrane filtration, liquid-
based preparations, and cell blocks. The sensitivity of micros-
copy can be improved by increasing the concentration of the
specimen. Specimens should be prepared soon after collection
to prevent degeneration. If this is not possible, refrigeration and/
or addition of equal volume of 50% alcohol can be used. At least
2–5 mL is required for bacterial culture and >10 mL for fungi
and/or mycobacteria because these latter organisms are gener-
ally present in low numbers.
●● Fine needle aspiration (FNA) permits procured material to be
immediately evaluated on site for appropriate triage. Aspirated
material can be used to make smears and liquid based prepara-
tions and cell blocks, or sent for culture, flow cytometry and
molecular studies. Material submitted for culture requires the

use of sterile containers into which patient’s material is added
along with minimal sterile saline. Isolation of pathogens in fine
needle aspirates is almost always considered significant and not
due to contamination.
Specimen Sites
●● Genital tract. Collection of genital specimens includes Pap
smears, swabs, Tzanck preparations of ulcers, and infrequently
FNA. Typically, specimens in female patients to detect patho-
gens are acquired at the time of performing a Pap test. Many
common and uncommon pathogens can be identified on a Pap
smear (see Chap. 5). A wet preparation can be used to make
a rapid diagnosis of vaginitis. A definitive diagnosis of certain
pathogens may require culture, especially in cases of suspected
sexual abuse.
●● Urinary tract. The normal urinary tract is usually devoid of
bacteria, except for microflora of the urethral mucosa. Never-
theless, urine can become contaminated with bacteria of the
vaginal canal or perineum. For urinary tract infections, a mid-
stream “clean-catch” urine specimen is preferable. A 24-h urine
sample is recommended for suspected schistosomiasis. Cath-
eterized urine can be collected, but not urine from catheter bags.
Other specimens from the urinary tract that may be required to
diagnose infection include suprapubic aspirates (used mainly in
neonates and small children), upper tract brushings and wash-
ings, urinary diversions (e.g., ileal conduit), and kidney FNA.
●● Respiratory tract. Sputum is often submitted for the diagnosis of
infection. Multiple, early morning specimens improve sensitivity
because they harbor pooled overnight secretions, and hence they
are more likely to contain concentrated bacteria. All cytopre-
paratory techniques (pick and smear, Saccomanno, cytocentrif-
ugation, liquid based) are suitable. Sputa should be processed
as soon as possible, because after 20 h of refrigeration there is
a significant decrease in recoverable organisms. For pneumo-
cystis, the yield from sputum is generally low. Various grading
schemes (e.g., Bartlett grading system, Murray and Washington
Specimen Sites 11
grading system) have been used to assess the quality of sputum

samples for Gram staining. These schemes use the number of
squamous epithelial cells and leukocytes as well as the presence
of mucus in sputum samples. For example, greater numbers of
epithelial cells indicates oropharyngeal contamination. These
grading schemes do not apply for all infections (e.g., Legionella
spp., mycobacteria, fungi, and viruses). Bronchial washings,
brushings, and bronchoalveolar lavage specimens are recom-
mended for the optimal recovery of microorganisms. Organisms
seen in sputum and specimens collected via bronchoscopy may
be present due to contamination from the oral cavity rather than
true infection of lungs. Transbronchial and percutaneous FNA
may be required in some patients.
●● Central nervous system. Specimens that can be submitted for
microbiology studies include CSF obtained by lumbar punc-
ture or other means (subdural tap, ventricular aspiration, or col-
lected from a shunt), stereotactic FNA (e.g., abscess), and tissue
biopsy. Specimens should be prepared as soon as possible after
collection. If this is not possible, addition of an equal amount
of 50% alcohol may help preserve the specimen. Refrigeration
may adversely affect the recovery of certain microorganisms.
Rapid diagnostic tests are available including India ink prepara-
tion for Cryptococcus neoformans and wet preparation for free-
living amebae. FNA may identify toxoplasmosis, mycobacteria,
cryptococcus, ameba, and cysticercosis.
●● Gastrointestinal system. A variety of cytologic specimens can
be obtained from the gastrointestinal tract including stool sam-
ples, ano-rectal swabs, secretions, and FNA. The development of
fiber-optic endoscopy has greatly expanded the ability to obtain
specimens for cytological evaluation (e.g., esophageal and gas-
tric brushings and washings), including endoscopic ultrasound
FNA of the liver and pancreas, as well as bile duct brushings.
●● Musculoskeletal system. Usually such specimens are obtained
by FNA, which includes aspiration of joint fluid. Joint fluid
clots quickly, and if not submitted into appropriate containers
that contain anticoagulant cell counts cannot be performed.
●● Skin. Cytologic specimens include superficial scrapings, swabs
and for vesicles, bullae, pustules, and deep palpable subcutane-
ous lesions FNA.
●● Fluids. Effusions due to bacterial infection (e.g., Staphylococcus

spp., Streptococcal spp.) appear turbid and purulent macroscop-
ically while mycobacterial-infected effusions often have a shiny
green appearance. Fungi (e.g., Candida, Cryptococcus) and par-
asites (e.g., Echinococcus, ameba, Strongyloides) may produce
a purulent or serous effusion, whereas viral infected-fluids (e.g.,
coxsackie, herpes) are usually serous.
Suggested Reading
Murray PR, Witebsky FG. The clinician and the microbiology laboratory.
In: Mandell GL, Bennett JE, Dolin R, editors. Principles and practice
of infectious diseases. 7th ed. Philadelphia: Churchill Livingstone
Elsevier; 2010. p. 233–65.
Winn W, Allen S, Janada W, Koneman E, Procop G, Schreckenberger P,
et al. Koneman’s color atlas and textbook of diagnostic microbiology.
6th ed. Philadelphia: Lippincott Williams & Wilkins; 2006. p. 67–110.
Woods GL, Gutierrez Y. Diagnostic pathology of infectious diseases.
Philadelphia: Lea & Febiger; 1993. p. 539–637.
3
Host Reactions to Infection
Sara E. Monaco1, Walid E. Khalbuss2,
and Liron Pantanowitz3
1–3
Pittsburgh, PA 15232, USA
The reaction of a human host to infectious stimuli can differ and

manifest in various ways (Table 3.1). These reaction patterns
depend on the target (i.e., organism or antigen) and immune status
of the patient. Knowledge of these reactions and their cytomorpho-
logic features can help identify potential infectious agents. Charac-
teristic host reaction patterns are the focus of this chapter.
Acute (Purulent) Inflammatory Response

●● An acute inflammatory exudate composed predominantly of
neutrophils.
●● An abscess is a localized area of liquefactive necrosis packed with
neutrophils associated with cell debris and often organisms.
●● This is a common response to bacterial or fungal organisms
(Fig. 3.1).
Cytomorphologic Features
●● Abundant neutrophils with degenerated cells and acellular
debris.
●● Examination at high power may reveal intracellular or extracel-
lular organisms, such as the negative image of mycobacteria
seen on Diff-Quik (DQ) stained smears within macrophages or
background material.

14 3. Host Reactions to Infection
Table 3.1. Different host reactions to infection.

Usual reactions and inflammatory patterns
Acute purulent inflammation
Eosinophilia and allergic mucin
Granulomatous inflammation
Necrosis
Viral cytopathic effect
Reactive epithelial atypia and mesenchymal repair
Unusual reactions and inflammatory patterns
Immune reconstitution inflammatory syndrome (IRIS)
Hemophagocytosis and emperipolesis
Ciliocytophthoria
Xanthogranulomatous inflammation
Malakoplakia
Pseudotumor/inflammatory pseudotumor reaction
Crystal formation
Inclusions in granulomatous inflammation
Splendore-Hoeppli phenomenon
Fig. 3.1. Acute suppurative lymphadenitis (Diff-Quik stain, high mag-

nification; inset: Pap stain, high magnification). The smears are cellular
and show numerous neutrophils in a background of acute inflammatory
debris.
Eosinophilia and Allergic Mucin 15
Differential Diagnosis
●● Cat scratch disease
●● Mycobacterial infection in children or immunocompromised
patients, when the body cannot mount a granulomatous response
●● Mimics include cellular degeneration, apoptosis (karyorrhectic
debris that mimics neutrophils), Kikuchi lymphadenitis, eosi-
nophilia (eosinophils mimic neutrophils, especially on Papani-
colaou stained smears)
Ancillary Studies
●● Special stains and/or immunostains for organisms
●● Microbial cultures
Eosinophilia and Allergic Mucin

●● This is a type I immediate hypersensitivity response that may
occur with allergies, parasites, and certain fungal infections.
●● It is typically seen in the nasal sinuses (rhinosinusitis) or lower res-
piratory tract (asthma, pulmonary infiltrates, and bronchiectasis)
(Fig. 3.2).
●● Viscous allergic mucin is seen with numerous eosinophils
and possibly Charcot Leyden crystals, which are needle or
rhomboid-shaped eosinophilic crystals.
●● Material should be carefully examined for fungus, particularly
Aspergillus spp.
●● Noninfectious inspissated mucin
●● Fungi other than Aspergillus such as mucormycosis and dema-
tiaceous fungi like Bipolaris spicifera or Curvularia lunata
Fig. 3.2. Charcot-Leyden crystals (Pap stain, high magnification). Needle-

shaped eosinophilic crystals are seen in association with numerous eosi-
nophils (inset), which have weakly orangeophilic cytoplasmic granules and
bilobed nuclei.
Ancillary Studies
●● Special stains (PAS, GMS) and/or immunostains for fungal
organisms
●● Fungal cultures
Granulomatous Inflammation
●● A chronic inflammatory response comprised of aggregates of
epithelioid macrophages (histiocytes) with or without other
inflammatory cells.
●● Granulomas can be subclassified into necrotizing (caseating
with central necrosis) and non-necrotizing (without central
necrosis) granulomatous inflammation.
Granulomatous Inflammation 17
●● Granulomas may form cohesive clusters of macrophages (e.g.,

tuberculoid leprosy, syphilitic gumma) or present as a diffuse
population of macrophages (e.g., lepromatous leprosy). Diffuse
macrophage infiltration is often seen in patients with impaired
cell-mediated immunity.
●● Granulomas with a polymorphous exudate that includes
neutrophils may be seen with tuberculosis, actinomycosis,
cysticercosis, filariasis, rhinosporidiosis and other fungal
infections.
●● Foreign body-type granulomas occur in response to parasitic
eggs or cuticular fragments or certain parasitic worms.
●● Epithelioid macrophages have kidney bean or boomerang-
shaped nuclei, prominent nucleoli, and abundant ill-defined
cytoplasm.
●● Multinucleated giant cells may be seen including Langhans
giant cells (with nuclei arranged around the periphery of the cell
in a horseshoe pattern) or foreign body-type giant cells (with
scattered nuclei).
●● There may be evidence of phagocytosis of microorganisms or
other debris within macrophages.
●● Intermixed inflammatory cells are usually lymphocytes and
plasma cells, but neutrophils may also be seen.
●● Aspirates may have suboptimal cellularity if procured from
long-standing hyalinized granulomas.
●● Necrotizing granulomatous inflammation: Mycobacterium
tuberculosis infection, fungal infection, cat-scratch disease.
●● Non-necrotizing granulomatous inflammation: Atypical myco-
bacterial infection (nontuberculous mycobacteria), fungal infec-
tion (Cryptococcus), sarcoidosis, foreign body.
●● Granulomatous inflammation with neutrophils: M. tuberculosis,
cat scratch disease, fat necrosis.
●● Granulomas associated with malignancy: Lymphoma, seminoma,

squamous cell carcinoma.
●● Xanthogranulomas (see uncommon host reactions).
●● Malakoplakia (see uncommon host reactions).
●● Mimics: low-grade neoplasia (e.g., renal cell carcinoma), spin-
dle cell neoplasms (e.g., spindle cell melanoma).
●● Pitfall: False positive diagnoses due to overcalling granulomas
as malignancy, particularly in cases of necrotizing granulomas.
Ancillary Studies
●● Special stains, immunostains, and/or PCR for organisms
●● Microbial cultures (Figs. 3.3–3.5 and Table 3.2)
Fig. 3.3. Multinucleated foreign body-type giant cell (Diff-Quik stain,

high magnification). A large cell with multiple scattered vesicular nuclei
within abundant ill-defined cytoplasm.
Fig. 3.4. Non-necrotizing granulomatous inflammation (Diff-Quik stain,
high magnification). Cohesive cluster of macrophages seen in an atypical
mycobacterial infection. Note the negative image (clear rods) of mycobac-
teria seen within the histiocytes and in the background.
Fig. 3.5. Necrotizing granulomatous inflammation (Pap stain, medium

magnification). Cohesive granulomas (left) are present in a background of
necrotic inflammatory material (right).
20
3.
Table 3.2. Cytomorphology of granulomatous and reactive host reactions compared to neoplasia.
Cytomorphologic features Granulomatous inflammation Reactive atypia Neoplasia
Cellularity Mild–moderate Low–moderate Usually high
Range of cell types Continuum (benign to reactive) Continuum (benign to reactive) Two populations (normal
and tumor)
Multinucleated giant cells Frequent Uncommon Uncommon
Host Reactions to Infection
Nuclei Boomerang to oval with smooth Smooth nuclear membrane Large with irregular
contours nuclear membrane
Nucleoli Present in epithelioid macrophages Uniform and small Prominent and irregular
Cytoplasm Vacuolated and ill-defined Depends on cell type, often dense Scant cytoplasm
squamoid with scalloped edges
Background Necrotic or non-necrotizing Clean or inflammatory Necrotic
Necrosis 21
Necrosis
●● Necrosis is the end result of cell death and an irreversible form
of cell injury that occurs with benign conditions (infection,
inflammation, infarction) and neoplasms (Fig. 3.6).
●● The gross appearance of aspirated necrosis is thick yellow-tan,
pus-like material. It is often easy to make smears with necrotic
material. More peripheral sampling of a lesion may be required
to see viable material.
●● Necrotic material forms amorphous, somewhat granular, thick
acellular debris, which can form linear rolls or lines on the slides
in some cases. Necrotic material may exhibit variable staining
with different stains.
Fig. 3.6. Necrosis (Pap stain, low magnification). Necrotic acellular

debris with a granular appearance can clump in a linear arrangement when
smeared on slides.
●● Coagulative necrosis contains ghost cells that have loss of nuclei

but preserved cell shape.
●● A careful search for microorganisms, atypical or tumor cells is
important.
●● Necrotizing granulomatous inflammation
●● Fat necrosis
●● Tumor necrosis
●● Inspissated cyst contents
●● Postprocedural necrosis (after previous FNA biopsy). Be cautious
not to over-interpret reactive atypia in a necrotic background
Ancillary Studies
Viral Cytopathic Effect

●● Viruses can induce cellular changes associated with infection
that may result in nuclear and/or cytoplasmic structural changes
or inclusions. These are degenerative changes often associated
with viral replication or cell lysis.
●● Nuclear changes may include nuclear enlargement (e.g., cytome-
galovirus), smudgy chromatin (e.g., adenovirus in bronchial
epithelial cells), glassy chromatin (e.g., human polyoma virus
in urine), multinucleation (e.g., herpes simplex virus), large
prominent macronucleolus (e.g., owl eye appearance of cytome-
galovirus), intranuclear inclusions (margination of chromatin or
eosinophilic Cowdry bodies seen with Herpes simplex virus), or
koilocytic change (human papillomavirus in cervical Pap tests).
Reactive Epithelial and Mesenchymal Repair 23
●● Cytoplasmic changes may include giant cell formation and

intracytoplasmic inclusions (e.g., respiratory syncytial virus and
measles in respiratory samples).
●● Nuclear changes may be more easily appreciated on alcohol-
fixed Pap stained slides than air-dried Diff-Quik or Romanowsky
stained slides.
●● Treatment (radiation, chemotherapy) related change
●● Degenerative change, which usually lacks multinucleation and
inclusions
●● Malignancy
Ancillary Studies
●● Immunocytochemical stains for viral infections
●● Serology for viral infections
Reactive Epithelial and Mesenchymal Repair

●● Reactive atypia or repair includes squamous metaplastic or other
epithelial atypia (e.g., of bronchial epithelium), mesenchymal
spindle cells with atypia, and granulation tissue.
●● These changes can occur in response to certain infections (e.g.,
cavitary fungal lesions, chronic abscess, or in response to ulcer-
ation), but may also be seen after treatment (radiation, chemo-
therapy) or infarction (Fig. 3.7 and Table 3.2).
●● Specimens display a continuum of changes from benign cells to
cells with reactive or repair features. Unlike neoplasms there is a
lack of two distinct populations (i.e., normal and tumor cells).
●● Atypical cells have uniform nuclear membranes, occasional
small nucleoli, and collectively exhibit uniform repair-type
atypia (“school of fish” appearance) often with cohesive cell
Fig. 3.7. Reactive epithelial atypia (H&E stain, high magnification). In

this bronchoalveolar (BAL) specimen, all of the squamous cells show
similar cytologic atypia in association with an Aspergillus infection (upper
right).
groups and maintenance of polarity. High cellularity, loss of

cohesion, three-dimensional cell groups, irregular nuclear con-
tours, increased nuclear-to-cytoplasmic ratios, and many mitoses
are concern for malignancy.
●● The background can be inflammatory and necrotic, particularly
with cavitary infections.
●● Reactive cellular atypia unrelated to infection (e.g., infarction)
●● Chemotherapy or radiation effect
●● Malignancy
Ancillary Studies
Immune Reconstitution Inflammatory Syndrome 25
Reactions with Impaired Cell-Mediated Immunity

●● In patients with impaired cell-mediated immunity (e.g., AIDS),
their immune system cannot effectively kill microbes or form
granulomas. As a result, the host reaction to infection in these
patients is often atypical.
●● Host response to infection in these cases may result in (a) no or
scant inflammation (e.g., Cryptococcus and Pneumocystis jirovecii
infection), or (b) a diffuse infiltration of macrophages that are
packed with numerous intracellular organisms (e.g., Mycobacte-
rium avium-intracellulare, leishmaniasis, histoplasmosis).
●● Microorganisms like yeast may be seen without associated
inflammatory cells.
●● Samples may contain diffuse sheets of macrophages with abun-
dant foamy cytoplasm and numerous organisms.
●● Granulomatous inflammation
●● Conditions with numerous foamy histiocytes such as fat necrosis,
lipoid pneumonia, and Gaucher disease
●● Malignant histiocytosis
Ancillary Studies
Immune Reconstitution Inflammatory Syndrome

●● The immune reconstitution inflammatory syndrome (IRIS) is a
florid inflammatory response that may occur in HIV infected
patients shortly after starting highly active antiretroviral therapy
(HAART).
●● IRIS is usually triggered in HIV-positive individuals who have
an underlying coinfection (e.g., tuberculosis, CMV, Cryptococ-
cus) or disease (e.g., Kaposi sarcoma).
●● Clinically it presents as a paradoxical worsening of disease or

pre-existing infection in HIV patients, shortly after starting antiret-
roviral treatment. This may be a life-threatening condition.
●● Marked florid granulomatous inflammation or other inflamma-
tory response.
●● Microorganisms may not be identified at the site of inflamma-
tion.
●● Newly acquired infection
Ancillary Studies
●● Concomitant drop in HIV levels with improvement in CD4 cell
count
Hemophagocytosis and Emperipolesis

●● Hemophagocytosis is the ingestion and often destruction of
blood cells by macrophages. Emperipolesis is the penetration of
an intact cell into and through a larger phagocytic cell.
●● Hemophagocytic syndrome is due to activated macrophages in
different organs that phagocytose other cells such as red blood
cells (RBCs) and lymphocytes.
●● This host reaction can be seen with a viral-associated (second-
ary) hemophagocytic syndrome (EBV, HIV, CMV, Parvovirus
B19), as well as a variety of other noninfectious primary (famil-
ial) clinical disorders like hemophagocytic lymphohistiocytosis
(HLH). Some gene mutations have been implicated (e.g., such
as perforin, IL-2, and purine nucleoside phosphorylase).
●● Hemophagocytosis is not specific and can be seen in up to 50%
of patients with bone marrow examination as part of a workup
for fever (Fig. 3.8).
Hemophagocytosis and Emperipolesis 27
Fig. 3.8. Hemophagocytosis (Diff-Quik stain, high magnification).

acrophages are shown with engulfed intracytoplasmic red blood cells
M
and a surrounding clear halo.
●● The hallmark finding is macrophages with abundant cytoplasm
and peripherally located ingested RBCs or leukocytes.
●● Phagocytosed cells may be intact or fragmented, and with
emperipolesis may be surrounded by a thin cytoplasmic mem-
brane or halo.
●● Histiocytes are immunoreactive with CD68 and S100, but are
negative for CD1a.
●● Sinus histiocytosis with massive lymphadenopathy (Rosai-
Dorfman disease)
●● Noninfectious primary hemophagocytic lymphohistiocytsosis
(HLH)
●● Associated T-cell lymphoma
●● Malignant histiocytosis with atypical histiocytes
Ancillary Studies
●● Immunostains to characterize macrophages (S100 and CD68
positive)
●● Immunostains, serology and/or further microbiology studies to
detect an underlying viral infection
Ciliocytophthoria
●● Ciliocytophthoria refers to the finding of anucleate apical por-
tions of ciliated epithelial cells (also referred to as detached
ciliary tufts). This may be seen in respiratory, gynecologic and
peritoneal cytology specimens.
●● Ciliocytophthoria can occur as a result of certain viral infections
(e.g., adenovirus infection in the lung), but may also be trau-
matic in nature (Fig. 3.9).
●● Single or multiple detached tufts of cilia without nuclei.
Fig. 3.9. Ciliocytophthoria (Pap stain, high magnification). A detached

ciliary tuft is seen (arrow) in this sputum specimen.
Xanthogranulomatous Inflammation 29
●● Noninfectious cause such as idiopathic or traumatic etiology.
●● Mimics: Ciliated microorganisms (e.g., Balantidium coli), para-
sites, foreign material.
Ancillary Studies
●● Immunostain for viral infections (e.g., Adenovirus)
Xanthogranulomatous Inflammation
●● This is an uncommon form of granulomatous inflammation
characterized by many lipid-laden foamy macrophages.
●● Such inflammation mainly involves the kidney (xanthogranulo-
matous pyelonephritis) or biliary system (xanthogranulomatous
cholecystitis). It is often observed in patients with diabetes and/
or some other form of immunocompromise.
●● The condition is most commonly associated with Proteus,
Escherichia coli, or Pseudomonas spp. infection (Fig. 3.10).
●● There are numerous histiocytes with vacuolated or lipid-laden
cytoplasm (foam cells), as well as chronic inflammatory cells.
●● Occasionally multinucleated giant cells may be seen, including
Touton giant cells with nuclei placed around the periphery of
the cell.
●● Other granulomatous or histiocytic processes
●● Malignancy such as renal cell carcinoma or adenocarcinoma
Ancillary Studies
●● Gram stain for associated bacteria
positive)
Fig. 3.10. Xanthogranulomatous inflammation. FNA showing (left) a

predominance of foamy macrophages with ill-defined cytoplasmic bor-
ders (Pap stain, high magnification) that (right) form sheets in cell block
material (H&E stain, high magnification).
Malakoplakia
●● This is an uncommon chronic granulomatous inflammatory
reaction of unknown etiology, thought to be due to the inabil-
ity of macrophages to eliminate Gram-negative coliforms (e.g.,
E. coli or Proteus).
●● It commonly affects the genitourinary tract (bladder), but has
also been described in a variety of different tissues.
●● In the urinary tract, malakoplakia is associated mainly with
E. coli. Pulmonary malakoplakia is a known complication of
Rhodococcus equi pneumonia in AIDS patients.
●● Macrophages contain Michaelis-Guttman bodies, which are
thought to represent mineralized bacterial fragments (Fig. 3.11).
Malakoplakia 31
Fig. 3.11. Malakoplakia (H&E stain, high magnification; inset: Pap stain,
high magnification). Macrophages are shown with characteristic eosi-
nophilic cytoplasm and targetoid, round intracytoplasmic inclusions known
as Michaelis-Guttman bodies.
●● Specimens contain numerous macrophages (von Hansemann
cells) that have eosinophilic granular cytoplasm containing
cytoplasmic Michaelis-Guttman bodies.
●● Michaelis-Guttman bodies are round-to-oval, laminated inclu-
sions surrounded by a membrane or halo, that typically have
a calcified or clear core. These inclusions are usually PAS
positive, Grocott (GMS) positive, and von Kossa positive due to
their calcium composition.
●● Numerous bacteria may be seen among acute or chronic inflam-
mation.
●● Other infectious granulomatous disease (e.g., tuberculosis)
●● Intracellular yeast forms or other organisms
●● Foreign body-type granulomas with foreign material engulfed
●● Noninfectious granulomatous disease, particularly sarcoidosis
which may have similar Schaumann bodies (round, concen-
trically laminated calcium inclusions). The other inclusions
described with sarcoidosis are stellate-shaped asteroid bodies
and clear calcium oxalate Hamazaki-Wesenberg bodies
●● Psammomatous calcification
Ancillary Studies
●● Special stains for Michaelis-Guttman bodies (PAS positive,
GMS positive, von Kossa positive)
●● Gram stain to identify associated bacteria
positive)
●● Microbial culture (e.g., urine culture)
Inflammatory Pseudotumor Reaction

●● This rare mass lesion (pseudotumor) can be seen in any organ
tissue, commonly described in patients with HIV infection. The
clinical and imaging impression is often concern for malig-
nancy.
●● Such a localized inflammatory mass may develop in response to
a viral infection (e.g., CMV, EBV), mycobacteria, or parasite.
●● Cytology specimens contain a reactive spindle cell and/or
myofibroblastic proliferation with intermixed histiocytes and
inflammatory cells.
●● The inciting microorganism (e.g., parasitic worm) may be present.
Crystal Formation 33
●● Granulation tissue
●● Granulomatous inflammation
●● Spindle cell neoplasms: Renal cell carcinoma, melanoma, mesen-
chymal neoplasms including Kaposi sarcoma (LNA-1 immuno-
reactive for HHV8) and EBV-associated smooth muscle tumors
Ancillary Studies
●● Special stains for organisms (e.g., acid fast stains for mycobac-
terial spindle cell pseudotumor)
●● EBV in situ hybridization (EBER) positivity may be seen in
EBV-associated smooth muscle tumors
●● PCR for mycobacteria
●● Immunostains to characterize lesional cells (macrophages are
S100 and CD68 positive, ALK negative, and myofibroblastic
cells may express smooth muscle actin)
Crystal Formation
●● Charcot-Leyden crystals are seen in association with eosi-
nophilia. They consist of lysophospholipase, which is produced
by eosinophils, and results from the breakdown of eosinophils.
●● Birefringent calcium oxalate crystals may be seen in association
with Aspergillus infection, particularly with Aspergillus niger.
Crystals are believed to form when oxalic acid precipitates and
undergoes crystallization when produced via a fermentation
process by Aspergillus.
●● Calcium oxalate crystals form rosettes or wheat sheaf-like clus-
ters and polarize under polarized microscopy (Fig. 3.12).
●● Charcot-Leyden crystals are needle- or rhomboid-shaped eosi-
nophilic crystals seen in association with eosinophilic inflam-
mation (Fig. 3.2).
●● The background may be inflammatory or necrotic.
Fig. 3.12. Crystal formation in Aspergillus infection (Diff-Quik stain, high

magnification; Inset: polarization microscopy, high magnification). Acute
inflammatory cells and necrotic debris with fungal hyphal elements showing
narrow-angle branching (left) associated with calcium oxalate crystals (right).
●● Calcium oxalate crystals: Aspergillus spp.
●● Charcot-Leyden crystals: Eosinophilic inflammation (allergy,
asthma, parasites)
●● Other crystals or foreign material
Ancillary Studies
●● Special stains (PAS, GMS) for fungal elements
●● Fungal culture for Aspergillus spp.
Splendore-Hoeppli Phenomenon
●● The Splendore-Hoeppli phenomenon (also called asteroid
bodies) describes the formation of eosinophilic crystalline mate-
rial around microorganisms (fungi, bacteria, and parasites) or
biologically inert substances.
Splendore-Hoeppli Phenomenon 35
Fig. 3.13. Splendore-Hoeppli phenomenon (H&E stain, high magnifica-

tion). A case of Actinomyces infection in the bone in which an eosinophilic
stellate band can be seen at the edge of the filamentous organisms (sulfur
granule) and surrounding acute inflammatory cells.
●● These eosinophilic structures may be seen in association with

filamentous bacilli (actinomycoses, nocardiosis), other bacterial
infections (Staphylococcus aureus, Pseudomonas aeruginosa),
botryomycosis, schistisoma, and microfilaria.
●● The formation of this material is thought to be a localized host
reaction made up of glycoprotein or antigen-antibody com-
plexes, in addition to tissue debris and fibrin. This reaction
probably prevents phagocytosis and intracellular killing of the
insulting organism (Fig. 3.13).
●● The characteristic finding is a stellate or club-shaped acellu-
lar band-like structure surrounding microorganisms or sulfur
granules (in the case of actinomycosis), which separates them
from the background inflammatory cells and debris.
●● Foreign, crystalline, or necrotic material
●● Fibrin deposition
●● Tophaceous lesions of gout
●● Granulomatous inflammation with keratin debris
Ancillary Studies
●● Special stains for microorganisms
Suggested Reading
Brummer E. Human defenses against Cryptococcus neoformans: an
update. Mycopathologia. 1999;143:121–5.
Gupta M, Venkatesh SK, Kumar A, Pandey R. Fine-needle aspira-
tion cytology of bilateral renal malakoplakia. Diagn Cytopathol.
2004;31:116–7.
Hadziyannis E, Yen-Lieberman B, Hall G, Procop GW. Ciliocytophthoria
in clinical virology. Arch Pathol Lab Med. 2000;124:1220–3.
Kradin RL, Mark EJ. The pathology of pulmonary disorders due to
Aspergillus spp. Arch Pathol Lab Med. 2008;132:606–14.
Kumar N, Jain S, Murthy NS. Utility of repeat fine needle aspiration
in acute suppurative lesions: follow-up of 263 cases. Acta Cytol.
2004;48:337–40.
Pantanowitz L, Balogh K. Charcot-Leyden crystals: pathology and diag-
nostic utility. Ear Nose Throat J. 2004;83:489–90.
Pantanowitz L, Omar T, Sonnendecker H, Karstaedt AS. Bone marrow
cryptococcal infection in the acquired immunodeficiency syndrome.
J Infect. 2000;41:92–4.
Rodig SJ, Dorfman DM. Splendore-Hoeppli phenomenon. Arch Pathol
Lab Med. 2001;125:1515–6.
Sereti I, Rodger AJ, French MA. Biomarkers in immune reconstitution
inflammatory syndrome: signals from pathogenesis. Curr Opin HIV
AIDS. 2010;5:504–10.
Zeppa P, Vetrani A, Ciancia G, Cuccuru A, Palombini L. Hemophagocytic
histiocytosis diagnosed by fine needle aspiration cytology of the spleen:
a case report. Acta Cytol. 2004;48:415–9.
4
Microbiology
Liron Pantanowitz1, Gladwyn Leiman2, and Lynne S. Garcia3
1
2
Fletcher Allen Health Care, Professor of Pathology,
University of Vermont, Burlington, VT, USA
3
LSG & Associates, 512-12th Street, Santa Monica, CA 90402, USA
Cytologists are likely to encounter infectious diseases either

because a cytology sample was obtained for diagnostic purposes
or incidentally when an infectious process or microorganism is
discovered in the material they are reviewing. In order to render an
accurate diagnosis, and correctly identify clinically important spe-
cies or microorganisms, a good understanding and knowledge of
microbiology is essential. This chapter provides a broad overview
of microbiology that is relevant to the practicing cytologist, but is
not intended to replace standard microbiology texts.
Viruses
●● Viruses replicate only inside host cells. Their particles (called
virions) consist of DNA or RNA and a capsid (coat) that may
be surrounded by a lipid envelope. Once they attach to and pen-
etrate cells, they uncoat and replicate so that their progeny may
be released following host cell lysis.
●● Viral infection may cause cell death, proliferation, or neoplastic
transformation (oncogenesis) (Table 4.1). Tumor viruses may
promote cancer by expression of viral oncoproteins (or onco-
genes) and/or inactivation of tumor suppressor genes.

38 4. Microbiology
Table 4.1. Viral induced tumors.

Virus Tumor
Epstein-Barr virus (EBV) Non-Hodgkin lymphoma (e.g., Burkitt
lymphoma, post-transplant lymphoprolif-
erative disorder, plasmablastic lymphoma)
Hodgkin lymphoma
Carcinoma (e.g., nasopharyngeal carcinoma,
gastric carcinoma)
Smooth muscle tumor
Follicular dendritic cell sarcoma
Kaposi sarcoma herpesvirus/ Kaposi sarcoma
human herpesvirus-8 Non-Hodgkin lymphoma (e.g., primary
(KSHV/HHV8) effusion lymphoma)
Castleman disease
Human papillomavirus (HPV) Anogenital dysplasia and carcinoma
Oropharyngeal dysplasia and carcinoma
Hepatitis viruses (HBV, HCV) Hepatocellular carcinoma
Human T-cell lymphotropic virus Adult T-cell leukemia/lymphoma
type 1 (HTLV-1)
Merkel cell polyomavirus Merkel cell carcinoma
(MCPyV)
●● In general, viruses are too small to be identified directly by

light microscopy. Viruses that remain latent often do not cause
apparent changes to infected cells. However, several viruses
may cause cytopathic changes (Fig. 4.1) that affect the nucleus
(e.g., inclusions, margination, multinucleation), cytoplasm
(e.g., koilocytosis, syncytial giant cell formation), and/or entire
cell (e.g., cytomegaly, ciliacytopthoria). Recognition of these
changes can be life-saving as this would initiate confirmatory
studies and/or therapy (Fig. 4.2).
●● Superinfection by pyogenic bacteria is a complication of many
viral infections that may mask subtle viral changes.
Papillomaviruses
●● Papillomaviruses (genus) are nonenveloped viruses that contain
double-stranded circular DNA molecules that replicate exclusively
in skin and/or mucosal keratinocytes. They belong to the Papil-
lomaviridae family.
Viruses 39
Fig. 4.1. Viral cytopathic changes. (a) HPV showing a large binucleate
koilocyte and adjacent smaller high grade squamous intraepithelial lesion
(HSIL) cell. (b) Herpes simplex virus showing a large multinucleated
epithelial cell with cowdry A inclusions and a smaller cell with an intra-
nuclear cowdry B inclusion. (c) CMV infected cell showing enlarge-
ment (cytomegaly), an intranuclear inclusion (“owl’s-eye” appearance),
and intracytoplasmic inclusions. (d) Molluscum contagiosum infection
showing a keratinocyte with an intranuclear inclusion (molluscum body).
(e) Measles (or RSV) infected syncytial giant cell with intranuclear inclu-
sions. (f) BK polyomavirus infected epithelial cells (decoy cells) showing
early (ground glass) and late (“fish-net stocking”) intranuclear inclusions,
as well as a comet cell in the middle with eccentric cytoplasm. (g) Adeno-
virus infected pneumocytes showing “smudge cells” with inclusions fill-
ing the nucleus and decapitated ciliated cells (ciliocytophthoria).
●● Their genome is divided into an early (E) region that encodes

genes E1–E7, and a late region (L) that encodes the capsid genes
L1 and L2. In oncogenic human papillomavirus (HPV) types,
the genes E6 (binds to p53) and E7 (binds to retinoblastoma
[Rb] protein) are key players in transforming cells.
●● HPV infection causes various diseases including warts (ver-
ruca), anogenital lesions (condylomata acuminata, intraepi-
thelial neoplasia) and cancer, epidermodysplasia verruciformis
(genodermatosis), oral and laryngeal papillomas, as well as
orpharyngeal and conjunctival cancer. Genital HPV infection is
covered in greater detail in Chap. 5.
40 4. Microbiology
Fig. 4.2. Viral cytoplasmic inclusions. (Left) Cytomegalovirus infected

cells (MGG stain, high magnification). (Right) Measles infected cells
(Phloxine tartrazine stain, high magnification) (image courtesy of
Dr. Pawel Schubert, University of Stellenbosch, Cape Town).
Herpesviruses
●● Herpesvirues (family Herpesviridae) are DNA viruses that may
cause latent or lytic infections. Reactivation of latent viruses has
been implicated in a number of diseases.
●● A major hallmark of herpes infection is the ability to infect
mainly epithelial mucosal cells and/or lymphocytes. Cytomega-
lovirus (CMV) can infect many cells types including epithelial
cells, endothelial cells, neuronal cells, smooth muscle cells, and
monocytes.
●● There are eight types of herpesvirus that may infect humans
(Table 4.2). They include the Alphaherpesviruses (HSV and
Varicella-Zoster virus [VZV]), Betaherpesviruses (CMV,
HHV6, HHV7), and Gammaherpesviruses (Epstein-Barr virus
[EBV] and KSHV). EBV and KSHV are oncogenic.
●● Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) have
similar characteristics. Viral infection typically results in the
Table 4.2. Human herpesviruses (HHV).
HHV type Virus name Target cells Disease
HHV1 Herpes simplex virus type 1 (HSV-1) Mucoepithelium Oral and/or genital herpes
HHV2 Herpes simplex virus type 2 (HSV-2) Mucoepithelium Oral and/or genital herpes
HHV3 Varicella-Zoster virus (VZV) Mucoepithelium Chickenpox
Shingles
HHV4 Epstein-Barr virus (EBV) Lymphocytes and epithelium Infectious mononucleosis
Non-Hodgkin lymphoma
Hodgkin lymphoma
Nasopharyngeal carcinoma
Lymphomatoid granulomatosis
Gastric carcinoma
Oral hairy leukoplakia
HHV5 Cytomegalovirus (CMV) Epithelium, monocytes, lymphocytes Acute (mono-like) illness
Systemic illness (e.g., pneumonia, hepatitis)
Retinitis
HHH6 Roseolovirus T lymphocytes and others Sixth disease (roseola infantum or exanthem
subitum)
HHV7 Human herpes virus-7 (HHV-7) T lymphocytes and others Sixth disease (roseola infantum or exanthem
subitum)
HHV8 Kaposi’s sarcoma-associated herpes Lymphocytes and endothelium Kaposi sarcoma
virus (KSHV) Non-Hodgkin lymphoma
Viruses
Multicentric Castleman disease

41
42 4. Microbiology
formation of Cowdry type A and B inclusions. Both types of

HSV can infect oral (e.g., cold sores) or genital mucosa. HSV-2
is normally spread sexually, which is why genital herpes is usu-
ally the result of HSV-2 infection. Infection may also cause
herpes keratitis, gladiatorum (skin lesions), visceral and CNS
infection, and neonatal herpes.
●● VZV typically causes chickenpox (Varicella) in childhood and
shingles (Zoster) in adults, which is usually severe in patients
with acquired immunodeficiency syndrome (AIDS). Approxi-
mately 15% of patients may develop pneumonia. Infection in
utero can cause congenital varicella syndrome. The cytopathic
effect of VZV infection is similar to that seen with HSV.
●● EBV has a tropism for epithelial cells (e.g., oral and nasophar-
ynx) and B lymphocytes, binding to its receptor (CD21). Pri-
mary infection may cause infectious mononucleosis. Infected
B-cells activate T-cells, the cause of atypical lymphocytosis in
infectious mononucleosis. Latent infection in cells is charac-
terized by the expression of latent membrane proteins (LMP)
1 and 2, EBV nuclear antigens (EBNAs), and EBV-encoded
RNAs [EBERs]. EBV-associated malignancies are associated
with latent gene expression (Table 4.3).
●● CMV is the largest virus to infect humans. It produces cytome-
galic cells with characteristic “owl’s eye” nuclear inclusions.
Most infections are asymptomatic. However, in immunosup-
pressed persons CMV can be a major problem. CMV pneu-
monia is the most common life-threatening complication after
transplantation.
●● Human herpes virus 6 and 7 (HHV6 and HHV7) both infect T cells.
They cause sixth disease typically in children, where a transient
skin rash on the trunk and neck follows an episode of fever.
●● Kaposi’s sarcoma-associated herpes virus/Human herpes-
virus-8 (KSHV/HHV8) was the eighth herpes virus to be dis-
covered. Most viral genes are expressed in lytic infection. The
five genes expressed in latent infection are key to oncogenesis,
which includes the latency-associated nuclear antigen (LANA).
The immunohistochemical stain LNA-1 targets LANA within
the nuclei of KSHV infected cells. KSHV has an etiologic role
in Kaposi sarcoma, certain lymphomas like primary effusion
lymphoma (PEL), and multicentric Castleman disease.
Table 4.3. Patterns of latent gene expression in EBV.
Latency I Latency II Latency III
Nasopharyngeal
EBV gene Acute infection Burkitt lymphoma Hodgkin lymphoma carcinoma PCNSL PTLD
EBNA1 + + + + + +
EBNA2 + − − − + +
EBNA3 + − − − + +
LMP1 + − + + + +
LMP2 + − + + + +
EBER + + + + + +
PCNSL primary central nervous system lymphoma; PTLD post-transplant lymphoproliferative disorder
Viruses
43
44 4. Microbiology
Respiratory Viruses
●● Influenza and Parainfluenza viruses can cause severe respira-
tory tract disease (e.g., pneumonia, bronchitis, and bronchioli-
tis). As infection usually does not cause characteristic cytologic
findings, the diagnosis requires isolation and identification of
the virus in the laboratory or a rise in serum antibodies.
●● Coronavirus causes illness ranging from the common cold to
severe acute respiratory syndrome (SARS). Respiratory samples
may show atypical reactive pneumocytes with or without back-
ground inflammation and marked fibrin exudate in cases with
diffuse alveolar damage (DAD).
●● Respiratory syncytial virus (RSV) causes lower respiratory tract
infections mainly in childhood. RSV belongs to the same Para-
myxoviridae family as measles (Rubeola) and mumps viruses.
Both RSV and measles pneumonia can cause multinucleated syn-
cytial giant cells containing intranuclear and inconspicuous usually
paranuclear cytoplasmic inclusions. Multinucleated giant cells are
usually rare, but when identified may contain up to 35 nuclei.
●● Adenoviruses. They were named after being first isolated from
adenoid samples. There are 55 described serotypes in humans
that cause respiratory tract infections (e.g., pharyngitis, pneu-
monia). Infection may also cause gastroenteritis, conjunctivitis,
hemorrhagic cystitis, meningoencephalitis, hepatitis, and dis-
seminated disease. Early infected cells may display small eosi-
nophilic inclusions. With late infection, basophilic intranuclear
inclusions eventually obscure the nucleus producing a charac-
teristic “smudge cell.”
Polyomaviruses
●● Most people are infected with these viruses and hence are serop-
ositive for polyomaviruses. These double-stranded DNA viruses
tend to only cause infection in immunosuppressed individuals,
and are all potentially oncogenic. They fall under the SV40
(Simian vacuolating virus 40) clade seen in monkeys, except for
Merkel cell polyomavirus.
●● BK virus (BKV) has a tropism for cells of the genitourinary
tract. BKV may cause nephropathy in 1–10% of renal transplant
Viruses 45
patients resulting in the loss of their renal allograft. Reactivation

in the kidneys and urinary tract results in shedding of infected
cells, virions, and/or viral proteins in the urine. Infection can
thus be diagnosed using urine cytology looking for cells with
polyomavirus inclusions of the nucleus, as well as PCR. BKV
may also cause ureteral stenosis in renal transplant patients and
asymptomatic hemorrhagic cystitis, usually after bone marrow
transplantation.
●● JC virus (JCV) may infect the respiratory tract, kidneys, or
brain. CNS infection can cause fatal progressive multifocal leu-
koencephalopathy (PML) in AIDS patients.
●● Merkel cell polyomavirus (MCV or MCPyV). This recently dis-
covered virus (in 2008) causes around 80% of Merkel cell car-
cinomas. Although lymphocytes may serve as a tissue reservoir
for MCV infection, only rare (approximately 2%) of hematol-
ymphoid malignancies show evidence for MCPyV infection by
DNA PCR.
Poxviruses
●● Molluscum contagiosum virus. Infection involves the skin and
occasionally the mucous membranes. There are four types of
MCV (MCV-1–4). Skin lesions are self-limited and pearly in
appearance with an umbilicated (dimpled) center. Infected cells
are characterized by molluscum bodies (also called Henderson-
Paterson bodies). Unlike herpes, this virus does not remain
latent. As patients do not develop permanent immunity, repeated
infections can occur.
Retroviruses
●● Retroviruses are enveloped viruses that belong to the viral family
Retroviridae. They are RNA viruses that replicate in host cells
using the enzyme reverse transcriptase to produce DNA from its
RNA genome. DNA is then incorporated into the host genome.
●● Human immunodeficiency virus (HIV), types 1 and 2. HIV
belongs to the retrovirus family. Infection causes AIDS. Details
are covered in greater detail in Chap. 13.
●● Human T-cell lymphotrophic virus (HTLV), types 1 and 2.
HTLV-1 is the first recognized retrovirus that causes adult T-cell
46 4. Microbiology
leukemia/lymphoma (ATLL). Infection may also be involved

in certain demyelinating diseases. Infected lymphocytes in the
peripheral blood produce characteristic “flower cells.”
Miscellaneous Viruses
●● Hepatitis viruses. Several viruses may cause hepatitis including
Hepatitis A (RNA picornavirus), Hepatitis B (DNA hepadnavi-
rus), Hepatitis C (RNA flavivirus), Hepatitis E (RNA calicivi-
rus), and Hepatitis D (Delta agent). They usually do not cause
viral cytopathic changes seen in cytology samples. However, in
liver tissue chronic hepatitis B virus (HBV) can cause a ground-
glass appearance of hepatocytes due to the accumulation of
HBsAg within the endoplasmic reticulum. Chronic infection
with HBV and hepatitis C (HCV) may lead to cirrhosis, liver
dysplasia, and ultimately hepatocellular carcinoma.
●● Parvoviruses. These are among the smallest known DNA viruses.
Parvovirus B19 (B19V) causes fifth disease (erythema infectio-
sum) and arthropathy. Infection of erythroid precursors in the bone
marrow may cause severe anemia characterized by giant normob-
lasts and intranuclear inclusions with a ground glass appearance
that tend to compress the chromatin against the nuclear mem-
brane. Cells with parvovirus B19 inclusions have been reported in
cytology fluid specimens from fetal cases with hydrops fetalis.
Bacteria
●● Bacteria (singular: bacterium) are single-celled microorganisms
that measure 0.5–5.0 mm in length. Mycoplasma spp. are among
the smallest bacteria. Bacteria have a wide range of shapes.
Most are spherical (cocci) or rod-shaped (bacilli), but they may
also be curved or spiral-shaped (e.g., spirochaetes, Helicobacter
pylori). Some bacteria are described as being coccobacilli
because they have the ability to exist as a coccus, bacillus, or
intermediate form (e.g., Haemophilus influenzae, Rhodococcus
equi, Bartonella spp.). Bacteria may also form pairs (e.g., dip-
loids), chains (e.g., Streptococcus), or clusters (e.g., Staphylo-
coccus). Some bacteria may also have flagella.
Bacteria 47
●● Anerobic bacteria do not need oxygen for growth. Some anerobes

die when oxygen is present (obligate anerobes), whereas others
will utilize oxygen if it is present (facultative anaerobes). They
are found in normal flora (e.g., Fusobacterium in the mouth,
Bacteroides fragilis in the large bowel, Lactobacillis in the
vagina). These bacteria can usually be isolated from abscesses,
aspiration pneumonia, empyema, and wounds. Material being
collected from sites that do not harbor indigenous flora (e.g.,
body fluids other than urine and fine needle aspirates) should
always be cultured for anerobic bacteria.
●● Bacteria, along with some fungi (mainly Candida spp.) and
archaea (single-celled microorganisms), make up the normal
human flora of the skin, mouth, gastrointestinal tract, conjunc-
tiva, and vagina (lactobacilli). Loss of normal flora may permit
the unfavorable growth of harmful pathogens that can lead to
infection.
●● Some bacteria form biofilms, which are bacterial aggregates
embedded within a self-produced matrix (slime). These bacte-
rial clusters, seen associated with amorphous mucoid material,
may be encountered in cytology specimens related to catheter
infections, Pseudomonas aeruginosa pulmonary infections in
cystic fibrosis, middle ear infections, joint prostheses, and dental
(gingival) disease.
Gram-Positive and Gram-Negative Bacteria

●● Bacteria can generally be divided into Gram-positive and
Gram-negative bacteria on the basis of their reaction to the Gram
stain. Most bacteria can be classified into one of the following
four groups: Gram-positive cocci, Gram-positive bacilli, Gram-
negative cocci, and Gram-negative bacilli.
●● Gram-positive bacteria stain dark blue (violet) by Gram staining
because they retain the crystal violet stain as a result of the abundant
peptidoglycan in their cell wall. Gram-positive cell walls typically
lack the outer membrane found in Gram-negative bacteria.
●● Gram-negative bacteria cannot retain the crystal violet stain.
Hence, they take up the counterstain (safranin or basic fuchsin)
instead and with Gram staining appear red or pink (Figs. 4.3
and 4.4).
48 4. Microbiology
Fig. 4.3. Bacteria divided according to their shape (cocci or bacilli),

Gram staining properties, and dependence upon oxygen for growth.
Mycobacteria
●● Mycobacteria are aerobic Gram-positive rod-shaped bacilli
that are acid–alcohol fast (so-called AFB) with acid fast stains
(Fite, Ziehl-Neelsen, Kinyoun, and auramine rhodamine stains).
Mycobacterium tuberculosis are strongly acid fast positive (stain
deep red), thin, and slightly curved bacilli that measure 0.3–
0.6 × 1–4 nm (Fig. 4.5). The bacteria of MAI are typically short
and cocobacillary like. Beading may be seen in some mycobac-
teria, which represents nonuniform staining of the bacillus. For
example, M. kansasii are characteristically long and broad and
exhibit a cross-banded or barred appearance.
●● Acid-fast staining of morphologically similar bacteria such as
Nocardia and Legionella is a possible pitfall in the cytologic
diagnosis of mycobacterial infection. Other organisms known to
be acid-fast positive include micrococcus species, the oocysts of
cryptosporidium species, Isospora belli, and sarcocystis.
●● Mycobacteria are grouped on the basis of their appearance
and rate of growth in culture (slow, intermediate, and rapidly
growing). According to the Runyon classification there are three
Bacteria 49
Fig. 4.4. Commonly encountered bacteria. (Top left) Lactobacilli are

shown in a Pap test associated with normal squamous cells. These were
discovered by the German gynecologist Albert Döderlein in 1892.
(Bottom left) Sarcina forms seen attached to an oral squamous cell in a
BAL specimen, showing its characteristic appearance in tetrads (buckets
of eight elements). This type of bacteria is frequently observed as a com-
mensal flora to the mouth (GMS stain, high magnification). (Top right)
Sputum showing Gram positive diplococci of Streptococcus pneumo-
niae (Gram stain, high magnification). (Bottom right) Lung abscess FNA
showing clusters of Gram positive Staphyloccus aureus (Gram stain, high
magnification).
slow growing groups (photochromogens that develop pigments

with light exposure such as M. kansasii and M. marinum, sco-
tochromogens which become pigmented in darkness such as
M. scrofulaceum, and nonchromogens such as M. avium complex
[MAC]). Rapid growers include M. chelonae and M. fortuitum.
●● For diagnostic and treatment purposes they can be classified
into three main groups:
M. tuberculosis complex. This includes M. tuberculosis, M. bovis,
M. africanum, M. microti, BCG and M. canetti. Infection causes

tuberculosis. The response to Bacillus Calmette-Guerin (BCG)
50 4. Microbiology
Fig. 4.5. Mycobacterium tuberculosis can be identified (a) with an acid

stain (Ziehl-Neelsen stain, high magnification) or (b) negative staining of
bacterial rods (Diff-Quik stain, high magnification).
vaccine in some infants and immunocomprised patients may

cause postvaccinial disseminated infection presenting with
lymphadenitis, osteomyelitis, and hepatic granulomas. BCG
vaccine contains attenuated live bacilli of M. bovis.
Mycobacterium leprae which causes leprosy (Hansen’s disease).
Nontuberculous mycobacteria (NTM), which include all of
the other mycobacteria. These are also known as atypical

mycobacteria, mycobacteria other than tuberculosis (MOTT),
or environmental mycobacteria. Infections with these myco-
bacteria are increasingly being seen in immunosuppressed
patients. Infection causes lung disease but may also dissemi-
nate to involve the hematopoietic system, gastrointestinal
tract, as well as skin and soft tissue. While most NTM can
be detected microscopically with an acid-fast stain, culture
and/or molecular studies may be required to identify these
species.
Bacteria 51
Filamentous Bacteria
●● Bacteria can be elongated to form filaments (e.g., Actinobac-
teria, Nocardia, Rhodococcus, Streptomyces, Actinomadura).
They can sometimes form complex, branched filaments that
morphologically resemble fungal mycelia (mass of branching
hyphae).
●● These bacteria are usually part of the normal oral flora. Most
infections are acquired by inhalation of the bacteria or via
trauma.
●● Actinomyces (genus) belong to the Actinobacteria (class of
bacteria). Infection (actinomycosis) with these Gram-positive
bacteria forms multiple abscesses and sinus tracts that may dis-
charge sulfur granules. Actinomycosis is most frequently caused
by Actinomyces israelii.
●● Nocardia (genus) are weakly-staining Gram-positive bacte-
ria that form partially acid-fast beaded branching filaments.
There are a total of 85 species, although Nocardia asteroides
is the species that most frequently causes infection (nocar-
diosis). Nocardial disease (norcardiosis) includes pneumonia,
endocarditis, encephalitis, and/or brain abscess, as well cuta-
neous infections such as actinomycotic mycetoma (Figs. 4.6
and 4.7).
Chlamydia
●● Chlamydiae are obligate intracellular Gram negative bacteria.
They are classified taxonomically into a separate order (Chlamy-
dia) because of their unique life cycle.
●● Organisms occur in two forms: an elementary body (0.3 mm)
that exists outside the host and infects host cells where it trans-
forms into a reticulate body (0.6 mm). Following replication,
new elementary bodies are released from the infected host cell
when it ruptures.
●● Chlamydia inclusion bodies may be identified within infected
cells. However, the cytologic findings (e.g., in a Pap test) are not
considered reliable. When stained with iodine, reticulate bodies
can be visualized as intracytoplasmic inclusions. They can also
52 4. Microbiology
Fig. 4.6. Nocardia. (Top left) Diagrammatic illustration of branched

filamentous bacteria. (Top right) Negative image of Nocardia in a direct
smear from a brain abscess (Diff-Quik stain, high magnification). (Bottom
left) Nocardia bacteria are shown highlighted with a GMS stain (high
magnification). (Bottom right) Weakly Gram positive Nocardia (high
magnification).
be stained with Giemsa or Gimenez methods as well as immu-

nocytochemistry.
●● Organisms are better detected by culture (gold standard) or other
laboratory tests (e.g., enzyme immunoassay, leukocyte esterase
test in urine, rapid Chlamydia test, and nucleic acid tests).
●● Three species of Chlamydia are known to produce human disease:
Chlamydia pneumonia (also Chlamydophila pneumoniae
and previously known as the TWAR agent). Infection causes

pharyngitis, bronchitis, and atypical pneumonia. Less com-
mon infections include meningoencephalitis, arthritis, and
myocarditis. An association with atherosclerosis and possibly
lung cancer has been reported.
Bacteria 53
Fig. 4.7. Actinomyces. (Top left) Clump of long filamentous bacteria are
shown (May-Grünwald-Giemsa stain, high magnification). (Top right)
Actinomyces from the mouth contaminating a bronchoalveolar lavage
ThinPrep specimen (Pap stain, high magnification). (Bottom left) Typi-
cal “dust bunny” seen on a cervical Pap test (Pap stain; high magnifica-
tion). (Bottom right) Sulfur granule is shown in the center of the cell block
preparation aspirated from an actinomycotic liver abscess (H&E stain,
intermediate magnification).
Chlamydia trachomatis (previously called TRIC agent). This

includes three human biovars: trachoma (serovars A, B, Ba or
C), urethritis (serovars D-K), and lymphogranuloma venereum
(LGV, serovars L1, 2 and 3). Infection causes inclusion con-
junctivitis (trachoma), pneumonia in neonates, and sexually
transmitted disease in adults (e.g., cervicitis, urethritis, salp-
ingitis, proctitis, epididymitis).
Chlamydia psittaci (also called Chlamydophila psittaci)
causes respiratory psittacosis and is acquired from birds

(Fig. 4.8).
54 4. Microbiology
Fig. 4.8. Chlamydia. (Left) Chlamydia developmental cycle. Infectious

elementary bodies that infect a host cell (a) transform into noninfectious
reticulate bodies (b) which then multiply (c). Elementary bodies are then
released following cell lysis that can infect new cells (d). Chlamydia inclu-
sions containing (top right) elementary bodies (arrows) and (bottom right)
reticulate bodies (arrow) are shown in squamous cells of a Pap test (Pap
stain, high magnification).
Fungi
●● On the basis of morphologic forms fungi can be divided into
yeasts and hyphae.
●● Yeasts are unicellular fungi. They reproduce by budding (form-
ing blastoconidia) or fission. The term “yeast” is used only
to describe a morphological form of a fungus and is of no
taxonomic significance.
●● Hyphae (single hypha) are multicellular fungi. Morphologically
they are branching, thread-like tubular structures. Hyphae may
lack cross walls (coenocytic or aseptate) or have cross walls
(septate). A mold is a mass of hyphal elements (also called
mycelium).
Fungi 55
Fig. 4.9. Fungal morphology. Hyphae may be characterized as (a) pseu-

dohyphae (e.g., Candida spp.), (b) septate (e.g., Aspergillus) or (c) coeno-
cytic (aseptate) hyphae (e.g., Zygomycetes). Conidia (spores) develop from
asexual fruiting structures such as (d) a conidiophore or (e) enclosed in a
sac called a sporangium, in which case they are then called endospores.
●● Hyphae can produce conidia (synonymous with spores). Large

complex conidia are called macroconidia. Smaller more sim-
ple conidia are termed microconidia. When these conidia are
enclosed in a sac (the sporangium) they are called endospores.
A sporangium-bearing hypha is referred to as a sporangiophore.
●● Dimorphism (dimorphic fungi) is the condition whereby a fungus
can exhibit either the yeast form or the hyphal form, depending
on growth conditions (Fig. 4.9).
Candida
●● Candida is a polymorphic fungus that undergoes a yeast-to-
mycelial transition. In clinical specimens, they produce pseu-
dohyphae (hyphae that show distinct points of constriction
resembling sausage links), rarely true septate hyphae, and bud-
ding yeast forms (blastoconidia).
●● The yeast-like forms (blastoconidia) are oval and measure
3–5 mm in diameter
56 4. Microbiology
●● Although typically seen extracellularly, intracellular Candida

can mimic other small fungi such as Histoplasma. Candida usu-
ally exhibit variably sized yeast cells, lack a pseudocapsule,
and elicit more of a suppurative reaction than a granulomatous
response.
●● Candida yeasts form part of the normal flora on the skin and
mucous membranes of the respiratory, gastrointestinal, and
female genital tracts. They often contaminate cytology samples
from these sites. They may also colonize tissue (e.g., after pro-
longed antibiotic use, prolonged skin moisture, and in patients
with diabetes).
●● Infection may result from overgrowth or when introduced into
the body (e.g., intravenously). Superficial infections include
oropharyngeal and vulvovaginal candidiasis (thrush). Candi-
diasis may also become a systemic illness causing widespread
abscesses, endocarditis, thrombophlebitis, endocarditis, eye
infections, or involve other organs.
●● Candida albicans is clinically the most significant member of this
genus. Candida glabrata (previously known as Torulopsis glabrata)
is a nondimorphic species (only has a yeast form) (Fig. 4.10).
Cryptococcus
●● Cryptococci are small (5–15 mm) pleomorphic (ovoid to sphe-
roid) yeasts that are characterized by often having a thick gelatin-
like capsule and demonstrating narrow-based (teardrop-shaped)
budding. They have thin walls and are occasionally refractile.
Their capsules may have a diameter of up to five times that of
the fungal cell, and form a halo on Diff-Quik, Pap, and India
ink stains.
●● Smaller (2–5 mm) capsule-deficient cryptococci can resemble
other organisms with similar microforms (e.g., Histoplasma,
Candida, and immature spherules of Coccidioides immitis).
In such cases, with careful examination some weakly encap-
sulated yeasts can still be detected. Loss of capsular material
usually elicits an intense inflammatory reaction characterized
by suppuration and granulomas.
●● Yeasts usually produce single buds, but multiple buds and even
chains of budding cells may rarely be present.
Fungi 57
Fig. 4.10. Candida morphology. Pseudohyphae and yeast are shown of

(a) Candida albicans and (b) C. tropicalis. (c) C. glabrata (torulopsis)
only has a yeast form. The images of Candida on the right show classic
examples of (top) pseudohyphae with distinct points of constriction along
the fungal filaments, (middle) oval yeasts with a separate budding form
present in the top right field of the image, and (bottom) a germ tube (ger-
minating outgrowth) (GMS stains, high magnification).
●● The presence of pseudohyphae-like elements and germ tube-

like structures may be detected in some cases, mimicking
Candida. However, this is rare and reported to be observed
in older lesions of cryptococcosis where aberrant forms are
frequently seen.
●● Infection (cryptococcosis) arises mainly in immunosuppressed
patients and may cause very little inflammation.
●● Cryptococcus neoformans causes most infections, such as men-
ingitis and meningoencephalitis in HIV positive patients.
●● Cryptococcus gattii (formerly Cryptococcus neoformans var
gattii), endemic in tropical areas of Africa and Australia, may
cause cryptococcosis in immunocompetent individuals (Fig. 4.11).
58 4. Microbiology
Fig. 4.11. Cryptococcus. (Top left) Diagram showing the pleomorphic

yeast-like cells of C. neoformans, which have thin walls and exhibit narrow
based budding forming teardrop structures. (Top right) India ink prepara-
tion of a CSF specimen from a patient with AIDS associated cryptococcal
meningitis demonstrates unstained halos around the microorganisms due
to their thick capsules (high magnification). (Bottom left) A mucicarmine
stain demonstrates the mucinous capsules surrounding cryptococci (high
magnification). (Bottom right) Cryptococci are shown with ovoid and
cup-shaped forms that may resemble Pneumocystis organisms (Diff-Quik
Aspergillus
●● Aspergillus genus consists of many mold species. Pathogenic
species include Aspergillus fumigatus and Aspergillus flavus.
●● These fungi consist of septate hyphae that branch at 45° angles.
Other dichotomous hyphae that may mimic Aspergillus include
the hyalinohyphomyces (e.g., Fusarium, Penicillium) and der-
matophytes.
●● Species specific conidiophores called fruiting bodies have swollen
vesicles lined by phialides that give rise to many conidia. The pres-
ence of fruiting bodies in cytology samples are usually only seen
in samples obtained from cavities or other well oxygenated areas.
Fungi 59
Fig. 4.12. Fruiting bodies of Aspergillus spp. (Left). Illustrations of the

varied microscopic morphology of common Aspergillus spp. including
(a) A. nidulans and A. terreus, (b) A. fumigatus, (c) A. niger, (d) A. glaucus
group, (e) A. flavus, and (f) A. clavatus. (Right) Fruiting body of A. fumi-
gatus is shown in a ThinPrep BAL specimen from a patient with a cavitary
lung lesion (Pap stain, high magnification).
●● Diseases caused by Aspergillus spp. (aspergillosis) include

sinusitis, allergic bronchopulmonary aspergillosis, aspergilloma
(“fungus ball”) within lung cavities, and invasive disseminated
aspergillosis (Figs. 4.12 and 4.13).
Zygomycetes
●● The zygomycetes belong to the phylum Zygomycota (Table 4.4).
The two orders that contain fungi causing human disease are
the Mucorales and Entomophthorales. Most illness is linked to
Rhizopus spp. of the Mucorales.
60 4. Microbiology
Fig. 4.13. Aspergillus hyphae with branching at 45° angles are shown
(top left) in a ThinPrep specimen (Pap stain, high magnification), (top
right) direct smear (Pap stain, high magnification), (bottom left) with a
PAS stain (high magnification), and (bottom right) in a cell block (H&E
Table 4.4. Zygomycetes taxonomy.

Phylum Zygomycota
Class Zygomycetes
Order Mucorales Entomophthorales
Family Mucoraceae Cunninghamellaceae
Genus Absidia Mortierellaceae Ancylistaceae
Apophysomyces Saksenaceae Basidioboaceae
Mucor Syncephalastraceae
Rhizomucor Thamnidaceae
Rhizopus
Fungi 61
●● Zygomycetes are fungi characterized by the formation of spores

(zygospores) and a vegetative mycelium. They have broad,
ribbon-like, aseptate hyaline hyphae (coenocytic hyphae) with
wide-angle branching. These morphological features are helpful
in differentiating the zygomycetes from other fungal agents of
infection that may be seen in cytologic specimens (Table 4.5).
●● In cytology samples hyphal forms may be twisted, collapsed, or
wrinkled making them hard to evaluate. Moreover, in tissue sec-
tions from biopsies or cell block material, folds and creases in the
section may cause the hyphae to appear as if they have septae.
●● In respiratory samples, the zygomycetes can be distinguished
from dimorphic fungi and yeasts as they do not produce a yeast
phase in this anatomic site.
●● Samples are often associated with extensive necrosis and inflam-
mation.
●● Their isolation in the clinical laboratory reflects either environ-
mental contamination or clinical disease (zygomycosis). Human
zygomycosis is usually an opportunistic infection in immuno-
compromised hosts such as patients with diabetes mellitus, neu-
tropenia, or using immunosuppressive therapy.
●● Infection is associated with angioinvasive disease causing
thrombosis, tissue infarction, and subsequent dissemination.
●● Disease manifestations include rhinocerebral and pulmonary
disease, and infrequently cutaneous, gastrointestinal, and allergic
diseases (Fig. 4.14).
Dimorphic Fungi
●● Dimorphic fungi can exist both as a mold form that consists of
hyphae (when grown at room temperature outside the host) and
as yeast (when grown at body temperature in the host). There-
fore, in clinical samples obtained from patients the cytologist
will encounter yeasts from these organisms (Table 4.6). Several
such fungal species are potential pathogens.
●● Blastomyces. The yeasts are 8–15 mm in size, have a double-
contour refractile wall, and demonstrate broad-based budding.
The most well-known species of this genus is Blastomyces
dermatitidis, endemic to the United States (especially the
southeastern, south central, and midwestern states) and Canada.
62
4.
Table 4.5. Comparison between zygomycetes, Aspergillus spp., and Candida spp.
Morphologic feature Aspergillus Zygomycetes Candida
Microbiology
Pap stain appearance
Hyphal type Septate Aseptate Pseudohyphae

Hyphal width Consistently thin (2–3 mm wide) Variable and wide (6–16 mm wide) Consistently thin (2–3 mm wide)
Branching 45° angles 90° angles Variable angles
Blastoconidia Absent Absent Present
Sporulation Present with air exposure Absent Absent
Fungi 63
Fig. 4.14. Zygomycetes. (Left and top right) Zygomycete hyphae are
shown characterized by broad, aseptate (coenocytic) hyphae that dis-
play wide-angle branching (Pap stain, left high magnification, top right
intermediate magnification). (Bottom right) Fungal hyphae are shown
immunoreactive with a specific immunostain for zygomycetes (high
magnification).
Infection (blastomycosis) occurs by inhalation of the fungus

from its natural soil habitat. Infection may involve virtually any
organ including the lungs, skin, bones, and brain (Fig. 4.15).
●● Coccidioides. This fungus presents with endospores contained
within thick-walled spherules that vary in size (20–150 mm).
Endospores measuring 3–5 mm may be seen scattered singly if
the spherule ruptures. When free endospores occur within mac-
rophages, they can imitate other intracellular yeasts. The causa-
tive agents of infection (coccidioidomycosis) are C. immitis
and C. posadasii. These fungi are endemic in American deserts.
Infection causes granulomatous and miliary disease affecting
largely the lungs. In endemic regions, fungus balls may develop
within lung cavities.
64
4.
Table 4.6. Morphology of commonly encountered yeasts and yeast-like cells.

Fungi Yeast appearance Yeast shape Yeast size (mm) Associated elements Budding Location
Microbiology
Candida Oval 3–5 Pseudohyphae Narrow based Mainly extracellular

Rare hyphae
Histoplasma Oval to round 2–4 No hyphae Narrow based Mainly intracellular
Cryptococcus Oval to round 5–15 Very rare Narrow based Extracellular and
pseudohyphae intracellular
Blastomyces Spherical 8–15 No hyphae Broad based Mainly intracellular

Fungi Yeast appearance Yeast shape Yeast size (mm) Associated elements Budding Location
Coccidioides Oval 3–5 Within spherules None Mainly extracellular
Sporothrix Round to elon- 3–5 Rare hyphae Narrow based Mainly extracellular
gated
Pneumocystis Round to 5–8 No hyphae None Mainly extracellular

crescent
Penicilliosis Round to 2–3 Rare hyphae None Mainly intracellular

elongated
Fungi
65
66 4. Microbiology
Fig. 4.15. Dimorphic fungi including (a) Blastomyces dermatitidis,

(b) Coccidioides immitis, (c) Paracoccidiodes brasiliensis, (d) Histoplasma
capsulatum, and (e) Sporothrix schenckii.
●● Paracoccidioides. These yeasts measure 5–30 mm in size and

are round to oval. Budding is characterized by a central yeast
with multiple surrounding daughter buds, that morphologically
resembles a “ship’s wheel.” Infection (paracoccidioidomyco-
sis) is caused by Paracoccidioides brasiliensis, typically found
in Brazil and elsewhere in South America. Primary infection
(Valley Fever) is usually mild and self-limiting, but may progress
into a systemic mycosis producing oral lesions, generalized lym-
phadenopathy, and miliary pulmonary lesions. Infection can also
spread to bones, meninges, and the spleen.
●● Histoplasma. This budding yeast is round to oval, on aver-
age 1–5 mm in size and observed mainly within macrophages
(Fig. 4.16), but sometimes also within neutrophils. Narrow based
round to oval budding may be noted, but because of their small
size buds are often not seen. Intracellular yeasts are usually sur-
rounded by a clear zone (halo). However, with cell disruption
organisms may be spilled extracellularly. This fungus is usually
found in bird and bat (guano) fecal material. There are a few
Fungi 67
Fig. 4.16. Histoplasmosis. Numerous small intracellular and extracellu-

lar yeasts of H. capsulatum are shown (GMS stain, high magnification).
s pecies including H. capsulatum. H. capsulatum var. capsulatum

are smaller (1–5 mm) than H. capsulatum var. duboisii which have
larger sized budding yeast cells (5–12 mm). Although this fungus
occurs worldwide, it is prevalent in certain regions (Ohio and Mis-
sissippi river valleys) of North America and in caves of southern
and East Africa. Infection causes histoplasmosis which primarily
affects the lungs and mediastinum, but may become disseminated
presenting with hepatosplenomegaly, lymphadenopathy, ocular
and skin disease, as well as enlarged adrenal glands.
●● Sporothrix. Yeasts measure 3–5 mm in diameter, are round to
cigar-shaped, and can show single or multiple buds. Rarely
aseptate hyphae may be observed. The only active species is
Sporothrix schenckii, which is the causative agent of sporotri-
chosis (rose-handler’s disease). Initial cutaneous infections may
spread via lymphatics and disseminate to joints, bones, and the
central nervous system. Inhaled fungi can cause pulmonary spo-
rotrichosis with lung nodules, cavities, fibrosis, and hilar lym-
phadenopathy.
68 4. Microbiology
●● Penicillium. These fungi produce penicillin. Penicillium marn-

effei is the only known thermally dimorphic species. In cytology
specimens, Penicillium present in the mold phase with septate
and branched hyphae represent a contaminant. However, in
immunosuppressed patients P. marneffei is an opportunistic
infection that causes penicilliosis. There is a particularly high
incidence of penicilliosis in AIDS patients from tropical South-
east Asia. Infection after inhalation spreads from the lungs to
involve the hematopoietic system and skin. Yeast-like cells are
present within macrophages and extracellularly. They are not
true yeast cells, but rather arthroconidia. Intracellular “yeasts”
measure 2–3 mm in diameter and are round to oval. Because
they divide by binary fission, budding is not observed. The
extracellular organisms tend to be more elongated, sometimes
up to 13 mm, and can have “septae” (crosswalls from binary
fission).
Pneumocystis
●● Pneumocystis jirovecii (previously called Pneumocystis carinii)
is a yeast-like fungus of the genus Pneumocystis, which is the
causative organism of Pneumocystis pneumonia (or pneumocys-
tosis, formerly referred to as PCP).
●● The cysts often collapse forming crescent-shaped bodies.
●● All stages of the life cycle are found within the lung alveoli.
Once inhaled, unicellular trophozoites (1–4 mm, Giemsa posi-
tive) undergo binary fission to form a precyst (difficult to dis-
tinguish by light microscopy) and ultimately develop thick
walled cysts (5–8 mm, GMS positive). Spores (eight) form
within these cysts, which are eventually released on rupture of
the cyst wall.
●● This organism is often seen in the lungs of healthy individuals,
but is an opportunistic pathogen in immunosuppressed people,
especially those with AIDS.
●● Extrapulmonary disease may be seen with advanced HIV infec-
tion presenting with involvement of the lymph nodes, spleen,
liver, bone marrow, gastrointestinal tract, eyes, thyroid, adrenal
glands, kidneys, and within macrophages in pleural effusions
(Fig. 4.17).
Fungi 69
Fig. 4.17. Pneumocystis. (Top left) Diagram illustrating P. jirovecii thick

walled cysts with a diameter (5 mm) approximately equal to that of a red-
blood cell. When collapsed, some cysts assume a cup or crescent shape
(crushed ping-pong ball appearance). (Bottom left) Schematic showing the
ultrastructure of a cyst: The cyst wall is composed of an outer and inner
layer that is focally thickened (a). The center of the cyst contains a tro-
phozoite (b) with an ill-defined nucleus. (Top right) Bronchial washing
from a patient showing a foamy alveolar cast containing Pneumocystis
cysts (Pap stain, high magnification). (Bottom right) Localized areas of
cyst wall thickening are best seen with a GMS stain also highlighting their
central trophozoites (high magnification).
Dematiaceous Fungi
●● The dematiaceous (naturally pigmented) group of fungi pro-
duce melanin in their cell walls. As a result, fungal colonies
are brown when cultured and in tissue samples fungal forms are
characteristically pigmented. A Fontana-Masson stain can be
used to confirm the presence of fungal melanin pigment.
70 4. Microbiology
●● They cause several human infections including chromoblasto-

mycosis (also called chromomycosis) and phaeohyphomycosis
(or phaeomycotic cyst).
Dermatophytes
●● Dermatophytes cause infections of the skin and hair (ringworm
or tinea) as well as the nails (onychomycosis). The three genera
that cause these diseases include Microsporum, Epidermophy-
ton, and Trichophyton.
●● A rapid scraping of the nail, skin, or scalp can be used to iden-
tify characteristic hyphae and sometimes spores associated with
squamous cells or within broken hairshafts.
Hyalohyphomycoses
●● Hyalohyphomycosis is the term used to group together inva-
sive mycotic infections caused by hyaline septate hyphae. This
includes species of Aspergillus, Penicillium, Paecilomyces,
Acremonium, Beauveria, Fusarium, and Scopulariopsis. They
may represent contamination or cause invasive disease in the
immunosuppressed host.
●● Fusarium hyphae are similar to those of Aspergillus, with septate
hyphae that branch at acute and right angles. Sporulation may
also occur in tissue with infection (fusariosis). Their macroco-
nidia are crescent-shaped, orangeophilic, and septate structures
that measure 80–120 × 3–6 mm in size.
Parasites
Protozoa
●● Protozoa are unicellular motile organisms. They are tradition-
ally divided according to their means of locomotion such as
amebae, flagellates, and ciliates.
●● Their life cycle often alternates between trophozoites (feeding–
dividing stage) and cysts (dormant stage able to survive outside the
host). Their characteristics (particularly the nuclei and cytoplasmic
inclusions) help in species identification. Ingested cysts cause infec-
tion by excysting (releasing trophozoites) in the alimentary tract.
Parasites 71
●● Amebae (Sarcodina) pathogenic to humans include intestinal

and free-living amebae.
Intestinal amebae. Entamoeba histolytica causes amebiasis
that may manifest with dysentery, flask-shaped colon ulcers,

a colonic ameboma, and possible extraintestinal abscesses
that contain anchovy paste-like material within the liver, and
infrequently spleen or brain. Several of the amebae such as
Entamoeba dispar are harmless and some may be relatively
common, such as Entamoeba gingivalis that is usually found
in the mouth. Unlike other amebae, the cytoplasm of patho-
genic E. histolytica contains ingested red blood cells.
Free-living amebae. These include Acanthamoeba spp., Balam-
uthia mandrillaris, and Naegleria fowleri. Acanthamoeba

cause granulomatous amebic encephalitis (GAE), contact lens-
associated Acanthamoeba keratitis, and skin lesions. Balam-
uthia also causes GAE. N. fowleri (“brain-eating” ameba) is
associated with rapidly fatal primary amebic meningoencepha-
litis (PAM), most often seen in children swimming in fresh
water ponds and rivers during which amebae enter the nasal
passages and migrate to the brain via the olfactory nerve.
These trophozoites can be seen in CSF specimens, but culture
on nonnutrient agar plates seeded with Escherichia coli and/or
a flagellation test is required for confirmation.
●● Flagellates (Mastigophora) are organisms that have one or more
flagella.
Giardia. There are approximately 40 species described, but
the species that infects humans is Giardia lamblia (also

called G. intestinalis or G. duodenalis). This parasite is the
most common cause of protozoal gastroenteritis (giardiasis).
Trophozoites (9–21 mm long and 5–15 mm wide) are kite (or
pear)-shaped and have two nuclei, four pairs of flagella, and
two central axonemes running down their middle. Their cysts
(8–14 × 7–10 mm) seen in stool specimens are oval, thick walled,
and contain four nuclei and multiple curved median bodies.
Trichomonas. There are several trichomonad species such as
the intestinal Pentatrichomonas hominis which is a nonpath-

ogenic organism. Trichomonas vaginalis is the anaerobic,
flagellated protozoan that causes trichomoniasis (Fig. 4.18).
Details of this sexually transmitted infection are covered in
Chap. 5. Apart from urogenital infections, T. vaginalis has
72 4. Microbiology
Fig. 4.18. Trichomonas vaginalis. (Top left) Illustration showing an oval

organism (5–30 mm wide) that possess four anterior flagella, an undulat-
ing membrane, single large nucleus, and a central axostyle that projects
from the posterior end. (Bottom left) Trichomonas organisms are shown
in a sputum smear (indicated by black bars) with an oval shape and vis-
ible nuclei. Note that some of the squamous epithelial cells have typical
perinuclear “trich halos” (Pap stain, high magnification) (image cour-
tesy of Rafael Martinez Girón, Instituto de Piedras Blancas-Asturias,
Spain). (Right) Several trichomonads are shown (top right) free in the
background and (bottom right) attached to a squamous epithelial cell in a
ThinPrep cervicovaginal Pap test (Pap stain, high magnification).
also been reported to cause pneumonia, bronchitis, and oral

lesions. Pulmonary trichomoniasis is usually caused by aspi-
rated Trichomonas tenax (mouth commensal) and less often
T. vaginalis infection. An association between flagellated
protozoa and asthma has been reported.
Leishmania. These parasites are acquired from the sandfly.
Depending on the species, they may cause cutaneous (e.g.,

oriental sore), mucocutaneous (espundia or uta), or visceral
(kala-azar) leishmaniasis (Table 4.7). There are two mor-
phological forms: promastigote (with a flagellum) found in
Parasites 73
Table 4.7. Comparison of skin, mucocutaneous, and visceral leishmaniasis.

Pathogenic species
Type of infection Old world New world Geographic location
Cutaneous L. major L. mexicana South America, Middle
L. tropica East; North America
L. aethiopica (Southwestern USA)
Mucocutaneous None L. braziliensis South America, China
Visceral L. donovani None All continents except
complex Australia
the insect host and an amastigote (without flagella) present

in the human host (Fig. 4.19). Diagnostic samples may be
procured from skin lesions (cutaneous or mucocutaneous)
or bone marrow aspirates (visceral). The morphologic hall-
mark is the presence of multiple small (2–5 mm) intracellular
amastigotes within macrophages (Leishman-Donovan bod-
ies). Amastigotes are spherical to ovoid in shape and have
both a nucleus and ovoid or rod-shaped kinetoplast. The
differential diagnosis for multiple small organisms within
histiocytes includes H. capsulatum (with budding and only
intracellular) and toxoplasmosis (more curved and mostly
extracellular).
Trypanosoma. The major human diseases caused by trypano-
somatids are African trypanosomiasis (sleeping sickness)

caused by Trypanosoma brucei and American trypanosomia-
sis (Chagas disease) caused by T. cruzi. Trypomastigotes
(30 mm in length) are usually found in peripheral blood. They
have an undulating membrane, central nucleus, and kineto-
plast at the anterior end.
●● Ciliates (Ciliophora) include the parasitic species Balantidium
coli, the only member of this phylum known to be pathogenic
to humans. The trophozoite is relatively large (50–70 mm), has
a ciliated surface, and contains a kidney bean-shaped macro-
nucleolus. The cyst form may occasionally also have cilia.
Cilicytophthoria may be sometimes mistaken for these ciliated
organisms.
74 4. Microbiology
Fig. 4.19. Leishmania. (Top left) Life cycle showing the transition from
a flagellated promastigote that occurs in the sandfly to small amastig-
otes without flagella in the human host: Promastigotes phagocytosed by
macrophages multiply within these cells and disseminate when released.
(Bottom left) Illustration of an ovoid amastigote shows a large nucleus
and prominent rod-shaped kinetoplast. (Right) This FNA sample obtained
from a Saudi Arabian child presenting with hepatosplenomegaly and
lymphadenopathy from kala-azar shows few scattered amastigotes (arrows)
among chronic inflammatory cells (Giemsa stain, high magnification).
Apicomplexans
●● The Apicomplexa are a diverse group of protists that includes
organisms such as coccidia (Sporozoa), Plasmodium spp. (cause
malaria), and Babesia (cause babesiosis). Malaria and babesiosis
are not discussed further because the diagnosis and speciation
of these organisms primarily requires examination of peripheral
blood smears and monoclonal antibody tests.
●● Coccidian diseases include cryptosporidiosis (Cryptosporidium
spp.), isosporiasis (I. belli), cyclosporiasis (Cyclospora caye-
tanensis), sarcocystis, and toxoplasmosis (Toxoplasma gondii).
Parasites 75
The microsporidia, at one time a separate group (not coccidian),

are now classified with the fungi.
●● Cryptosporidium spp. C. parvum is the causative agent of crypt-
osporidiosis in humans and animals, a major cause of protracted
diarrhea in patients with AIDS. Other species that cause human
disease include C. hominis. These small (8–15 mm) oval para-
sites are identified within the brush border of the intestinal
epithelium, and are discussed in the chapter on gastrointesti-
nal infections. Ultrastructural studies have shown them to be
intracellular but with an extracytoplasmic localization in ente-
rocytes. Modified acid-fast thick-walled oocysts (4–6 mm) may
be detected in stool samples. Cryptosporidium can disseminate
beyond the intestine, especially in patients with AIDS, to involve
the biliary tract, stomach, lungs, middle ear, and pancreas.
●● Microsporidia include Enterocytozoon bieneusi and Encepha-
litozoon intestinalis (previously Septata intestinalis). Although
these organisms are now considered fungi, parasitologists still
maintain them in most books. In cytology specimens obtained
from the small intestine, microsporidia appear as numer-
ous small intracellular organisms within the apical portion of
enterocytes. They stain well with Gram and silver stains (e.g.,
Warthin-Starry). Their spores (1–1.5 mm) may be found with a
modified trichrome stain in stool samples as well as urine.
●● I. belli and Sarcocystis infections very rarely have trophozoites
that are detected. Their oocysts, however, may be seen when
excreted in feces.
●● T. gondii belongs to the genus Toxoplasma. Although infec-
tion can be acquired from the accidental ingestion of infective
oocysts from cat feces (definitive host), most infections are
acquired from eating infected rare or raw meats. Disease
ranges from mild flu-like illness to fatal fetal infections.
Latent infection may reactivate in immunosuppressed patients.
Organisms may be found in samples from the brain, heart,
eye, hematopoietic system, and lungs. Specimens may con-
tain free (extracellular) tachyzoites which are small (3–5 mm),
curved (banana-shaped) forms (Fig. 4.20). When parasites
accumulate within macrophages (so-called “bag of parasites”)
they form a pseudocyst (parasitophorous vacuole) containing
bradyzoites.
76 4. Microbiology
Fig. 4.20. Toxoplasma gondii. (Top left) Diagram showing crescent

shaped tachyzoites (sometimes called endozoites) with a prominent
nucleus: These trophozoites usually have a tapered anterior end and more
blunt posterior end. (Top right) Free tachyzoites (arrows) can be seen
in this BAL specimen (Giemsa stain, high magnification). (Bottom left)
Diagram showing a macrophage with a pseudocyst containing multiple
bradyzoites: Note that some of these microorganisms are still crescent
shaped. The cysts are usually round in brain tissue, more elongated in
muscle, and often very small and hard to identify in lung tissue. (Bottom
right) An infected macrophage contains a cluster of bradyzoites (Pap
Helminths
●● Helminths (parasitic worms) are categorized into three groups:
cestodes (tapeworms), nematodes (roundworms), and trema-
todes (flukes) (Table 4.8). Flukes and tapeworms belong to the
phylum platyhelminthes (flatworms).
●● Clinical infection may be caused by adult worms, larvae, and/or
eggs (Fig. 4.21). Infections are usually diagnosed by the charac-
teristics of these different developmental stages.
Table 4.8. Common parasitic worms (helminthiases).
Helminth Worm Egg
Cestodes (tapeworms)
Taenia saginata (beef tapeworm) Scolex with four suckers and proglottids Radially striated wall (30–40 mm)
Taenia solium (pork tapeworm) Scolex with four suckers, Radially striated wall (30–40 mm)
hooklets and proglottids
Diphyllobothrium latum (fish tapeworm) Scolex with wide proglottids Oval with operculum and knob at either
end (up to 60 mm)
Hymenolepis nana (dwarf tapeworm) Very small (2–4 cm) Wide inner and outer shells (30–47 mm),
contain polar filaments
Echinococcus spp. Protoscolices in hydatid cyst Identical to Taenia (30–45 mm)
Nematodes (round worms)
Trichuris trichiura (whipworm) Whip-like anterior end Barrel shaped with polar plugs at both ends
(20–50 mm)
Ascaris lumbricoides Large (up to 35 cm) Rough mammillated shell (up to 75 mm)
Necator americanus (hookworm) Mouthpart with cutting plates (adult worm) Thin wall with internal morula (35–75 mm)
Ancyclostoma duodenale (hookworm) Mouthpart with teeth (adult worm) Thin wall with internal morula (35–75 mm)
Strongyloides stercoralis Shorter buccal groove (mouth) Identical to hookworm (35–75 mm), rarely
than hookworm (rhabditiform larvae) seen
Enterobius vermicularis (pinworm) Pointed pin-like tail One side flattened (20–60 mm)
Trematodes (flukes)
Fasciola hepatica (liver fluke) Flat with cephalic cone Very large (up to 150 mm), operculated
(cannot distinguish from Fasciolopsis buski)
Fasciolopis buskii (intestinal fluke) Flat with pointed head Very large (up to 150 mm)
Parasites
Clonorchis sinensis (liver fluke) Flat with snout-like head Small with shouldered operculum (12–20 mm)
Paragonimus westermani (lung fluke) Flat ovoid worm Oval with shouldered operculum (45–120 mm)
77
78 4. Microbiology
Fig. 4.21. Parasitic eggs are shown in cytologic preparations. (Top left)
Enterobius vermicularis. (Top middle) Taenia (tapeworm). (Top right)
Trichuris trichiura. (Bottom left) Ascaris lumbricoides. (Bottom middle)
Schistosoma haematobium. (Bottom right) Pollen grain (belonging to the
Caryophyllaceae family) that may be mistaken for Toxocara eggs (images
courtesy of Dr. Pam Michelow, South Africa and Dr. Rafael Martinez
Girón, Spain).
●● The host response to these parasites includes eosinophilia, acute

inflammation, and sometimes granulomas.
●● Cestodes. These tapeworms usually parasitize humans after eating
underprepared meat such as pork (Taenia solium), beef (Taenia
saginata), or fish (Diphyllobothrium spp.), or food that is pre-
pared in conditions of poor hygiene (e.g., Echinococcus spp.).
Taenia. Infection with the adult tapeworms occurs follow-
ing ingestion of cysticerci in rare or poorly cooked beef or

pork. T. saginata (beef) infection results in small intestinal
infestation of adult worms (taeniasis). T. solium (pork) infec-
tion can also cause cysticercosis, as a result of the acciden-
tal ingestion of food or drink contaminated with tapeworm
eggs from the feces. Cysticercosis is characterized by cysts
Parasites 79
containing larvae located in several sites such as the brain

(neurocysticercosis causes seizures), eye, as well as muscles
and subcutaneous tissue (causes painful nodules). These
cysts may cause eosinophilia, an inflammatory reaction and
eventually they may calcify.
Echinococcus. Infection from the accidental ingestion of food
or drink contaminated with tapeworm eggs results in hydatid

disease, also known as echinococcosis. The larval cysts that
develop can be found in virtually any site, grow slowly, and
persist for many years until they cause symptoms or are
discovered incidentally. Disruption of a cyst containing highly
antigenic fluid may result in anaphylactic shock, and for this
reason it has been recommended that they should not be biop-
sied. However, on the basis of published data adverse reac-
tions are rare. Use of a fine gauge needle by a skilled operator
is important to prevent fluid leakage during aspiration. There
are three different forms of echinococcosis: cystic (unilocu-
lar) echinococcosis (caused by Echinococcus granulosus),
alveolar (multilocular) echinococcosis (caused by Echinoc-
occus multilocularis), and polycystic echinococcosis (caused
by Echinococcus vogeli and rarely Echinococcus oligarthus).
A hydatid cyst contains a thick outer (acellular) wall and thin
inner germinal epithelium. Alveolar and polycystic echinoc-
occosis cysts usually have multiple compartments. Hydatid
cysts may contain several liters of fluid, daughter cysts, and
hydatid sand (Fig. 4.22). Aspirated hydatid sand contains
protoscolices (future scolices) and free hooklets. Viable pro-
toscolices typically show a row of parallel hooklets whereas
dead ones contain haphazardly attached hooklets.
●● Nematodes. There are several roundworms (Table 4.7), but those
likely to be seen in cytology specimens are Enterobius vermicu-
laris, Strongyloides stercoralis, and the microfilariae.
E. vermicularis (pinworm, also known as the threadworm in
the United Kingdom) causes intestinal infestation (enterobia-

sis). The adult female worm migrates out onto the perianal area
at night, and once exposed to oxygen she lays her eggs. This
causes perianal pruritis and possibly vaginitis. Occasionally
subcutaneous perineal nodules may develop. In such cases, Pap
tests may contain an adult worm and/or eggs. The worm has a
80 4. Microbiology
Fig. 4.22. Echinococcus granulosus. (Left) (a) Diagram showing an adult

tapeworm that consists of a scolex (head) and three proglottids. The scolex
has suckers and a crown of hooklets (adult worm not found in humans).
Components of hydatid sand are illustrated including (b) evaginated
protoscolex (usually occurs when placed into saline), (c) invaginated
protoscolex with hooklets, (d) degenerated scolex with calcareous cor-
puscles, and (e) individual rostellar hooklets. (Top middle) Invaginated
protoscolex (Pap stain, high magnification). (Bottom middle) Evaginated
protoscolex (Pap stain, high magnification). (Far right) Free sickle shaped
hooklets (MGG stain, high magnification) (cytology images courtesy of
Pam M ichelow and Dr. Pawel Schubert, South Africa).
characteristic pointed tail (Fig. 4.23). Their eggs are colorless,

oval, thin walled, and flattened on one side,
S. stercoralis. This worm causes strongyloidiasis. After pen-
etrating the skin, infective larvae pass through the lung (Loef-
fler syndrome). They are then coughed or swallowed and infest
the duodenum. Here new autoinfective larvae may develop
(autoinfection) leading to chronic infection. In immunocom-
promised patients, larvae may penetrate the intestinal wall
Parasites 81
Fig. 4.23. E. vermicularis (pinworm). (Left) Diagram showing an adult

female worm (8–33 mm long × 0.3–0.5 mm wide) that has a cephalic infla-
tion and characteristic long, pointed tail. (Right) Pinworm shown among
neutrophils in a Pap test. If the morphology of the worm is not definitive,
then a diagnosis reporting a worm-like structure suggestive of pinworm is
appropriate (Pap stain, intermediate magnification).
and disseminate via the bloodstream (called hyperinfection).

Disseminated strongyloidiasis has a very high mortality rate.
Cytology specimens including gastrointestinal and pulmonary
(e.g., sputum) samples may contain larvae, either rhabditiform
(noninfective) or filariform (infective) types.
Filariae. These roundworms cause filariasis. Microfilar-
iae that may be periodically found in the peripheral blood

include Wuchereria bancrofti, Brugia malayi, and Loa loa.
W. bancrofti and B. malayi infest lymphatics leading to lym-
phadentitis and chronic lymphedema (elephantiasis). L. loa
resides in subcutaneous tissue and the conjunctiva. Certain
microfilariae such as Mansonella perstans, Onchocerca vol-
vulus, Dracunculus medinensis, and Dirofilaria immitis are
not readily found in blood smears. M. perstans inhabits body
cavities such as the peritoneum and pleura (serous cavity
filariasis). O. volvulus infects subcutaneous tissue forming
nodules and the conjunctivae causing blindness (onchocer-
ciasis or river blindness). D. immitis (dog heartworm) causes
granulomatous nodules in the lung. Microfilariae are the diag-
nostic forms of infection. The presence or absence of a sheath
82 4. Microbiology
and the pattern of nuclei in their tail are the main features
used to distinguish the various species. Occult filariasis has
been diagnosed by many bloody FNA procedures containing
microfilariae, worms, or even eggs. Filarial morphology is
best appreciated with a Giemsa stain. The background tissue
response in cytology aspirates may include eosinophils, neu-
trophils, chronic inflammation, and even granulomas.
●● Trematodes. The flukes are oval or worm-like helminthes that are
parasites of molluscs and vertebrates. The liver flukes include
Fasciola hepatica and Clonorchis sinensis that result in infesta-
tion of the bile ducts and subsequent biliary fibrosis. Infection
with C. sinensis is a risk factor for cholangiocarcinoma. Fasci-
olopis buskii is an intestinal fluke that infests both the bile ducts
and duodenum. Paragonimus westermani, the lung fluke, causes
lung infestation with pulmonitis. Also included are the schisto-
somes (blood flukes).
Schistosomes. Infection by these trematodes causes schis-
tosomiasis (bilharzia). There are three human schistosome

pathogens: Schistosoma mansoni from Africa (Nile delta)
which causes intestinal schistosomiasis, S. haematobium
from Africa and the Middle East that infests the urinary blad-
der, and S. japonicum from China and Southeast Asia that
primarily involves the liver. S. haematobium infection can
lead to squamous cell carcinoma of the bladder. Microscopic
identification of eggs in stool or urine specimens, as well as
tissue biopsies, can provide a rapid diagnosis. The spines
present on schistosome eggs help distinguish these different
species. The egg of S. haematobium (oval) has a terminal
spine, S. mansoni (oval) has a lateral spine, and S. japonicum
(round) has a small knob-like lateral spine.
Algae
●● Algae are ubiquitous and include a diverse group of simple
organisms that range from unicellular to multicellular forms.
The main algal groups include the cyanobacteria, green algae,
and red algae (e.g., dinoflagellates).
●● Most algae present in cytology samples are from contamination,
discussed in greater detail in Chap. 15.
Algae 83
Fig. 4.24. Prototheca. (Left) Diagram of protothecae demonstrating vari-

able morula formation: (Right) A sporangium of P. wickerhamii is shown
in which endospores have a moruloid (daisy-like) pattern (Pap stain, high
magnification) (image courtesy of Rafael Martinez Girón, Instituto de
Piedras Blancas-Asturias, Spain).
●● Prototheca is a genus of algae that lacks chlorophyll that causes

the disease protothecosis. Most human cases are caused by
P. wickerhamii. Infection may cause skin lesions or dissemi-
nated and systemic disease. Organisms may be seen within mac-
rophages or extracellularly. They form spherical sporangia that
range in size from 3 to 10 mm, have thick walls, and show no
budding. These morular forms often contain endospores arranged
symmetrically, typically in a daisy-like pattern (Fig. 4.24). They
stain with most stains including H&E, PAS, and GMS stains.
Suggested Reading
Ash LR, Orihel TC. Ash & Orihel’s atlas of human parasitology. 5th ed.
Chicago: American Society for Clinical Pathology Press; 2007.
Bayón MN, Drut R. Cytologic diagnosis of adenovirus bronchopneumo-
nia. Acta Cytol. 1991;35:181–2.
Bhambhani S, Kashyap V. Amoebiasis: diagnosis by aspiration and exfo-
liative cytology. Cytopathology. 2001;12:329–33.
84 4. Microbiology
Garcia LS. Diagnostic medical parasitology. 5th ed. Washington: ASM

Press; 2007.
Gupta N, Arora SK, Rajwanshi A, Nijhawan R, Srinivasan R. Histoplasmo-
sis: cytodiagnosis and review of literature with special emphasis on dif-
ferential diagnosis on cytomorphology. Cytopathology. 2010;21:240–4.
Kumar B, Karki S, Yadava SK. Role of fine needle aspiration cytology in
diagnosis of filarial infestation. Diagn Cytopathol. 2011;39:8–12.
Kumar PV, Omrani GH, Saberfirouzi M, Arshadi C, Arjmand F, Parhizgar
A. Kala-azar: liver fine needle aspiration findings in 23 cases presenting
with a fever of unknown origin. Acta Cytol. 1996;40:263–8.
Larone DH. Medically important fungi. A guide to identification. 3rd ed.
Washington: ASM Press; 1995.
Onuma K, Crespo MM, Dauber JH, Rubin JT, Sudilovsky D. Dissemi-
nated nocardiosis diagnosed by fine needle aspiration biopsy: quick and
accurate diagnostic approach. Diagn Cytopathol. 2006;34:768–71.
Sangoi AR, Rogers WM, Longacre TA, Montoya JG, Baron EJ, Banaei N.
Challenges and pitfalls of morphologic identification of fungal infec-
tions in histologic and cytologic specimens: a ten-year retrospective
review at a single institution. Am J Clin Pathol. 2009;131:364–75.
Takeuchi T, Fujii A, Okumiya T, Watabe S, Ishikawa T, Umeda A, et al.
The study of cytopathological aspects induced by human cytomegalo-
virus infection. Diagn Cytopathol. 2004;31:289–93.
Williamson JD, Silverman JF, Mallak CT, Christie JD. Atypial cytomor-
phologic appearance of Cryptococcus neoformans: a report of five
cases. Acta Cytol. 1996;40:363–70.
5
Gynecological Infections
Liron Pantanowitz1, R. Marshall Austin2,
and Pam Michelow3
1
2
Department of Pathology, Magee-Women’s Hospital of University of
Pittsburgh Medical Center, 300 Halket Street, Pittsburgh, PA 15213, USA
3
Cytology Unit, Department of Anatomical Pathology, University of the
Witwatersrand and National Health Laboratory Service, Johannesburg,
Gauteng, South Africa
Infections of the female genital tract, some of which are sexually

transmitted diseases (STDs), are common and hence an impor-
tant cause of morbidity and mortality for women worldwide
(Table 5.1). Women with infections of the lower genital tract may
be asymptomatic or present with vaginal discharge, bleeding,
dysuria, dyspareunia, abdominal pain, fever, malaise or manifest
with more severe systemic illness. Upper genital tract infections
often arise from ascending lower genital tract disease and their
sequelae may be serious including peritonitis, septicemia, infer-
tility, and ectopic pregnancy. Although Pap tests are primarily
used for the diagnosis of epithelial abnormalities, many infec-
tions can be diagnosed on cervical cytology. Women of all ages
infected with microbial agents have higher rates of atypical cer-
vical epithelial cells, including atypical squamous cells of unde-
termined significance (ASCUS) and squamous intraepithelial
lesions (SIL). This may be attributed in part to a greater predis-
position to human papillomavirus (HPV) infection, and hence the
development of cervical neoplasia in these women. This chapter
covers common and rare infections likely to be encountered on a
cervicovaginal Pap test. Infections of the vulva are covered in the
chapter with skin infections.

Table 5.1. Infections of the female genital tract.
Anatomical
location Infection Microorganisms
Vulva Viral Human papillomavirus (HPV),
Herpes simplex virus (HSV type I
and II), Molluscum contagiosum,
CMV, EBV
Bacterial Treponema pallidum (chancre,
condyloma lata), Corynebacterium
minutissimum (erthrasma), Haemo-
philus ducreyi (chancroid),
Chlamydia trachomatis (granuloma
inguinale), tuberculosis, Bartonella
henselae (bacillary angiomatosis)
Fungal Candida, Histoplasma capsulatum,
Cryptococcus neoformans,
dermatophytes
Parasites Enterobius vermicularis, Schistosoma
haematobium
Infestation Phthirus pubis (pubic lice), Sarcoptes
scabiei (scabies), myiasis
Cervix Viral HPV, HSV, CMV
and vagina Bacterial Neisseria gonorrheae, Gardnerella
vaginalis, Leptothrix, C.
trachomatis, Actinomyces
israelii, Mycobacterial infection,
Treponema pallidum
(syphilis), malakoplakia
Fungal Candida spp., Fusarium,
Aspergillus, Cryptococcus,
Histoplasmosis, Blastomyces,
Coccidioides, Paracoccidioides
Parasites Trichomonas vaginalis, Amebiasis,
S. haematobium, E. vermuclaris,
Echinococcus, Filaria,
Trypanosomes (Chagas disease),
Strongyloides, Taenia, Trichuris
trichiura, Ascaris lumbricoides
Upper Salpingitis, pelvic N. gonorrheae, C. trachomatis,
genital tract inflammatory Prevotella spp., Peptostreptococcus,
disease (PID), Bacteroides, Escherichia coli,
tubo-ovarian Haemophilus influenza, group B
abscess, streptococci, Actinmycosis,
endometritis Mycoplasma genitalium,
Mycobacterium tuberculosis,
Cryptococcus, Blastomyces,
Schistosoma, Enterobius,
Toxoplasma gondii, Entamoeba
histolytica, malakoplakia
Normal Flora 87
Inflammatory Changes
●● Acute inflammation. Various infectious agents may cause an
acute inflammatory infiltrate comprised of abundant neu-
trophils. However, the presence of neutrophils alone in Pap tests
does not necessarily indicate infection. If inflammatory changes
are marked and obscure the epithelial cells, the specimen may
be unsatisfactory for interpretation.
●● Follicular (lymphocytic) cervicitis. The formation of reactive lym-
phoid follicles in the subepithelium of the cervix may occasionally
be seen on a Pap test. It is more common in women who have an
atrophic cervix as the epithelium is thin, allowing the underlying
stroma to be sampled. Mature and immature lymphoid cells are
noted in addition to a few plasma cells and tingible-body macro-
phages. Follicular cervicitis is associated more often with Chlaym-
ida trachomatis than other infections of the cervix. The differential
diagnosis includes high-grade squamous intraepithelial lesion
(HSIL), endometrial cells, and non-Hodgkin lymphoma.
●● Epithelial change. Epithelial cells may show various degrees
of inflammatory and reparative change including cytoplas-
mic vacuolization, polychromasia, perinuclear halos, nuclear
enlargement, anisonucleosis, prominent nucleoli, mitoses, as
well as bi- and multinucleation. Reparative change can be dis-
tinguished from more severe (dysplastic or neoplastic) lesions
by the fact that cells showing repair show good cohesion,
flat monolayer sheets have a streaming appearance, maintain
polarity, and while they may have prominent nucleoli their
chromatin is evenly distributed within round, smooth, nuclear
membranes (Fig. 5.1).
Normal Flora
Microbiology
●● Lactobacillus (lactobacilli, formerly called Dőderlein bacilli)
are Gram-positive, anaerobic, lactic acid producing bacteria
normally found within the vagina (i.e., normal flora). Lactoba-
cilli such as Lactobacillus acidophilus maintain the acid vaginal
pH by converting cytoplasmic glycogen within intermediate
88 5. Gynecological Infections
Fig. 5.1. Inflammatory cells on Pap tests. (Upper left) ThinPrep Pap
test showing several pus balls characteristic of trichomoniasis (Pap stain,
intermediate magnification). (Bottom left) Follicular cervicitis seen on a
conventional Pap smear consists of polymorphous lymphocytes and sev-
eral tingible-body macrophages (Pap stain, high magnification). (Upper
right) This ThinPrep Pap test from a postmenopausal women with
follicular cervicitis shows a loose aggregate of lymphocytes in various
stages of maturation together with a tingible-body macrophage (Pap stain,
high magnification). (Bottom right) Cervix biopsy of follicular cervicitis
showing prominent subepithelial reactive lymphoid follicles with germinal
centers (H&E stain, low magnification; courtesy of Dr. Christopher Otis,
Tufts University School of Medicine, USA).
epithelial cells into lactic acid via proteolytic destruction

(cytolysis). This renders the vaginal environment hostile for
unwanted organisms. The normal vaginal flora does not extend
up into the sterile endometrium.
●● Loss of lactobacilli plays a role in the development of bacterial
vaginosis (BV) (so-called shift in flora) (Fig. 5.2).
Normal Flora 89
Fig. 5.2. Lactobacilli (high magnification images). (Top left) Thin bacilli
forming part of the normal flora are shown in this routine Pap test (Pap
stain, ThinPrep). (Bottom left) Multiple lactobacilli are seen coating
these two squamous epithelial cells, not to be confused with clue cells
(Pap stain). (Right) Long slender lactobacilli are seen associated with
cytolysis and bare nuclei (Pap stain, conventional smear).
Clinical Features
●● Common and normal finding in Pap tests. More common in the
second half of the menstrual cycle, during pregnancy, and in
patients with diabetes mellitus.
●● Decreased with BV.
●● Slender, rod-like bacilli can be seen lying in the background
and/or over the surface of cells.
●● Cytolysis results in free-lying bare nuclei and cellular debris of

intermediate squames mixed with lactobacilli.
Diagnostic Note
●● Lactobacilli can form long chains, not to be confused with
fungal hyphae.
●● Free-lying nuclei following cytolysis should be distinguished
from trichomonads, HSIL, endometrial cells, follicular cervicitis,
small cell carcinoma, and lymphoma.
●● Other sources of debris include atrophy and tumor diathesis.
●● Diagnostic ancillary tests are not required.
Leptothrix vaginalis
Microbiology
●● Leptothrix are long Gram positive anaerobic bacteria.
●● They are often associated with trichomonas infection (“spaghetti
and meatballs”).
Clinical Features
●● These bacteria are usually non-pathogenic on their own.
●● Long filamentous bacteria are seen that do not form spores.
Diagnostic Note
●● Compared to Actinomyces, Leptothrix are much less densely clus-
tered and are not associated with companion bacteria.
●● The finding of Leptothrix should encourage a thorough investi-
gation of the specimen for associated Trichomonas.
●● Ancillary tests are not required (Fig. 5.3).
Viral Infections 91
Fig. 5.3. Leptothrix (high magnification images). (Left) Leptothrix are

shown in this ThinPrep Pap test caught up with a few inflammatory cells
(Pap stain). (Top right) Long filamentous bacteria consistent with Lep-
tothrix are shown in a conventional Pap smear (Pap stain). (Bottom right)
Leptothrix are shown associated with several scattered trichomonads
(Pap stain).
Viral Infections
Human Papillomavirus (HPV)
Microbiology
●● Papillomaviruses are DNA viruses that belong to the family Papo-
viridae. They selectively infect skin and mucous membranes.
Genital HPV infection is almost exclusively sexually transmitted.
●● HPV is the dominant causative agent in anogenital warts, SILs,
and cervical carcinoma. Most HPV infections regress spontane-
ously. Persistence of oncogenic HPV infection is required for
progression to carcinoma.
●● There are over 100 different types of HPV. The types infect-
ing the female genital tract are divided into low- and high-risk
(HR). Low-risk (LR) HPVs are associated with condylomata
acuminata and LSIL, while the intermediate and HR oncogenic
HPV types are associated with LSIL, HSIL, and carcinoma.
LR HPV types include HPV 6, 11, 42–44, 53–55, 62, 66,

and 70.
Intermediate-risk HPV types include 31, 33, 35, 39, 51, 52,
54, 58, 59, 61, and 66–68.

HR HPV types include HPV 16, 18, 45, and 56.
●● HPV 16 accounts for most HPV-related vulvar cancers. HPV 18

accounts for a large proportion of cervical adenocarcinoma and
adenosquamous carcinoma.
●● Impaired patient immunity from HIV infection, transplantation,
or immunosuppressive drugs increases HPV persistence and
hence the development of CIN and cervical cancer.
Clinical Features
●● Initial infection is often asymptomatic.
●● Condyloma accuminatum (anogenital warts). In women, these
lesions usually initially involve the posterior introitus and nearby
labia. They can extend to other parts of the vulva, vagina, and
cervix. They can occur singly or in clusters and appear as flesh-
colored or pink polypoid or flat lesions.
●● SIL. SIL are asymptomatic. Mucosal lesions can be identified
after application of acetic acid and are best visualized on col-
poscopy. The older concept that SIL progress from low-grade
(LSIL) to high-grade (HSIL) lesions has now been replaced by
the concept that LSIL and many CIN2 lesions are nonprogres-
sive lesions and that true precancerous lesions (CIN3) develop
de novo in a subset of patients with persistent high-risk HPV
infection.
●● Cervical carcinoma. Early invasive carcinoma may be asymp-
tomatic. Later stages present with watery or blood-stained
discharge, postcoital bleeding, or spontaneous, irregular vaginal
bleeding but may present with advanced local disease or metas-
tases. In such cases the cervix may appear irregular, raised, red-
dened, or ulcerated.
●● HPV cytopathic effect includes koilocytosis and dyskeratosis
(atypical parakeratosis). In LSIL, koilocytosis is seen in inter-
mediate or superficial squamous cells (koilocytes) and includes
Viral Infections 93
Fig. 5.4. Koilocytosis (high magnification images). (Upper left) Koilo-

cytes in a ThinPrep Pap test with LSIL. Note the striking nuclear abnor-
malities in the koilocytes compared to the adjacent normal appearing
squamous cells (Pap stain). (Bottom left) A group of koilocytes with
prominent perinuclear halos and enlarged nuclei are shown in a conven-
tional Pap smear (Pap stain). (Upper right) Polka dot cells with intracyto-
plasmic eosinophilic hyaline globules (Pap stain). These cells more than
likely represent a degenerative process than an HPV effect associated with
condylomas as previously suggested. (Bottom right) Glycogenated squa-
mous cells mimicking koilocytes (Pap stain).
nuclear enlargement (3–4 times increase in size), hyperchromasia

with coarse granular to smudgy chromatin, and nuclear
irregularity (Fig. 5.4). Bi- and multinucleation is frequently seen,
but without molding of nuclei. Nucleoli are inconspicuous. The
perinuclear halo in LSIL cells tends to be well-defined.
●● HSIL, squamous cell carcinoma, and adenocarcinoma cells
related to HPV infection do not exhibit characteristic viral
changes. HSIL and squamous cell carcinoma may be keratiniz-
ing or nonkeratinizing (Fig. 5.5).
Fig. 5.5. High-grade squamous intraepithelial lesion (HSIL). This group

of dysplastic squamous cells has scant cytoplasm, irregular nuclear con-
tours, and hyperchromatic nuclei (Pap stain, high magnification).
Diagnostic Note
●● Detectable HPV does not always imply the presence of clinical
disease.
●● Squamous cells showing inflammatory changes may demon-
strate small clearings around the nucleus (perinuclear halo) and
enlarged nuclei. However, the nuclei in such reactive cells tend
to be more round and vesicular than in true koilocytes.
●● Navicular cells are boat-shaped squamous cells with an
intracytoplasmic vacuole containing glycogen. Empty vacu-
oles may resemble the halo seen in koilocytes, but the associ-
ated nuclear changes are not seen and the nucleus is usually
eccentric.
●● ASC-US is the term reserved for cells that are suggestive of, but
not diagnostic of, koilocytes.
●● Parakeratosis refers to small keratinized squames with
pyknotic nuclei. These cells and nuclei are much smaller than
koilocytes.
Viral Infections 95
Ancillary Tests
●● Several FDA-approved options exist for HPV testing using
cervicovaginal Pap test material. Several non-FDA-approved
options are also available for routine use, but caution must be
exercised as clinical validation of routine non-FDA-approved
routine HPV tests and for more novel HPV tests is very limited.
Direct probe methods include Southern, dot blot, and in situ
hybridization.
Signal amplification systems include hybrid capture like
the FDA-approved automated, qualitative Hybrid Capture

2 (HC2) assay (Qiagen, Netherlands) that detects inter-
mediate and HR HPV types. The Cervista High Risk HPV
test (Hologic Corp, Marlborough, MA, USA) is also FDA
approved in the USA.
Emerging test methods like microarrays and genotype assays.
●● Serology (e.g., anti-HPV L1 antibody) and HPV viral load have

been used to predict the development of CIN lesions (prognostic
markers).
●● Immunocytochemistry for surrogate biomarkers of HPV infec-
tion in dysplastic and cancer cells.
p16INK4a has high specificity for HPV transformed cells, but
may also stain nondysplastic cells (e.g., tubal metaplasia,

endometrial glandular cells) and, depending on the anti-
body clone, some microorganisms such as trichomonads
(Fig. 5.6).
Others including ProExC and Ki-67.
Herpes Simplex Virus (HSV)

Microbiology
●● Herpes simplex virus (HSV) is a double-stranded DNA virus
that belongs to the Herpesviridae family. Like other herpes
viruses, HSV can remain latent and re-activate. There is no dif-
ference between the cytology of primary and secondary genital
herpesvirus infection.
●● HSV include HSV-1 that primarily infects the oral cavity, eye,
central nervous system, and HSV-2 which infects the genital
tract. However, HSV-1 infection of the anogenital tract is not
Fig. 5.6. p16 immunocytochemistry (high magnification images). Thin-

Prep Pap test with (upper left) a group of HSIL cells (top left, Pap stain)
that shows nuclear and cytoplasmic immunoreactivity for p16 (bottom
left). Nonspecific staining with p16 (clone G175-405) is demonstrated with
(upper right) Trichomonas trophozoites and (bottom right) lactobacilli.
uncommon. The cytopathic effect due to HSV-1 and HSV-2 is

identical. Recurrent genital infection is mainly due to HSV-2
(Fig. 5.7).
Clinical Features
●● The first episode of genital herpes usually produces fever,
headache, and malaise. Genital symptoms include pain, dysuria,
vaginal discharge, tender inguinal lymphadenopathy, and vary-
ing stages of vesicles, pustules, and/or ulcers on an erythematous
base. Recurrent genital herpes is usually milder and shorter than
the first episode. Patients may remain asymptomatic, but infec-
tious. Complications of infection include local spread, extragen-
ital lesions, superinfection, and CNS disease (e.g., meningitis).
●● Transmission to neonates during vaginal delivery may cause
serious disseminated infection. A Cesarean section may therefore
Viral Infections 97
Fig. 5.7. Herpes (high magnification images). (Upper left) Conventional

Pap smear in a 16-year-old female showing many squamous cells with
Cowdry type B inclusions including nuclear molding, chromatin margina-
tion, ground glass nuclei, and (bottom left) prominent multinucleation
(Pap stain). (Upper right) Squamous cells in a ThinPrep Pap test with
eosinophilic intranuclear inclusions typical of Cowdry type A inclusions
(Pap stain). (Bottom right) Single dark stained cells with herpetic changes
may mimic HSIL (ThinPrep, Pap stain). Processing of liquid-based speci-
mens often causes increased numbers of isolated herpetic cells.
be preferentially performed if a mother about to deliver has

active genital herpes.
●● Infected squamous cells may show Cowdry type A inclusions
(eosinophilic intranuclear inclusions surrounded by a clear
zone) and/or Cowdry type B inclusions (nuclei molded rather
than overlapped, chromatin margination beneath the nuclear
membrane imparting a ground glass appearance to the nucleus,
and multinucleation).
●● A background acute inflammatory cell infiltrate may be marked.
Fig. 5.8. Mimics of Herpes (high magnification images). (Upper left)

Enlarged reactive multinucleated endocervical cell. Note the presence of
small nucleoli, a feature not seen in herpes (Pap stain). (Bottom left) Conven-
tional Pap smear showing neoplastic cells in a case of endocervical adenocar-
cinoma. Pale malignant nuclei demonstrate overlapping instead of molding
(Pap stain). (Upper right) A syncytiotrophoblast is shown in this Pap test from
a patient with a threatened abortion. The nuclei of this cell are overlapped and
have coarse chromatin. The background in this case contains trichomonads
and a few Leptothrix (Pap stain). (Bottom right) In this Pap test from a patient
with squamous cell carcinoma of the cervix the eosinophilic degenerated
tumor cell shows multinucleation and clearing of the chromatin (Pap stain).
Diagnostic Note
●● The Bethesda system interpretation is “Cellular changes con-
sistent with herpes simplex virus.”
●● Reactive endocervical cells with multinucleation may mimic
herpetic change. Neoplastic cells with multinucleation and/or
pale vesicular nuclei may also mimic herpes (Fig. 5.8). Other
mimics of herpes may include reactive/repair change, air-drying
artifact, cell distortion, and poor cell preservation.
●● The differential diagnosis for large multinucleated cells on
a Pap test includes giant cell macrophages (granulomatous
Viral Infections 99
inflammation, postpartum, after surgery), syncytiotrophoblast,

radiation or chemotherapy effect, macrocyte of LSIL, neo-
plasia (e.g., choriocarcinoma, MMMT), and B12 or folate
deficiency.
●● The diagnosis of herpes infection on a Pap test in a pregnant
patient close to delivery should be handled precipitously, which
may warrant a call to their healthcare provider so that appropri-
ate measures can be taken if necessary to avoid vertical trans-
mission of HSV to the neonate.
Ancillary Tests
●● Immunocytochemistry
●● HSV DNA detection by PCR or ISH
●● Serology (type-specific assays)
●● Viral culture
Cytomegalovirus (CMV)
●● Detection of cytomegalovirus (CMV) cytopathic effect in cervi-
cal Pap tests or biopsy is rare. CMV typically involves endocer-
vical glandular epithelium, and less commonly squamous cells.
●● The characteristic viral cytopathic change includes cytomegaly
with an intranuclear inclusion surrounded by a halo (“owl’s-eye”),
which can be confirmed using immunocytochemistry if necessary.
Molluscum contagiosum (Fig. 5.9)

Microbiology
●● This is a contagious viral infection caused by a DNA poxvirus.
Of the four types of MCV, MCV-2 is often sexually transmitted.
Clinical Features
●● Infection with M. contagiosum is common in the pubic area, and
infrequently affects the vagina and cervix.
●● Infection occurs after trauma to the skin or mucosa. Persist-
ent and disseminated infection occurs in immunosuppressed
patients like those with HIV coinfection.
Fig. 5.9. Molluscum contagiosum. Conventional Pap smear showing

(left) a group and (right) single infected squamous cells with typical mol-
luscum bodies. The bloody background has only few inflammatory cells
(Pap stain, high magnification).
●● Lesions may be variable in number and cutaneous dome-shaped

papules and nodules may appear umbilicated.
●● Infected squamous cells show characteristic cytoplasmic inclu-

sions called molluscum bodies. Inclusions may be eosinophilic
or basophilic in appearance. The nuclei of infected cells are
pushed to the periphery and therefore often inconspicuous.
●● There is usually little or no background inflammation.
Diagnostic Note
●● Molluscum bodies may mimic CMV intranuclear inclusions.
●● As this viral infection is recognized as being an STD, slides
should be carefully screened for the presence of other STDs.
●● Ancillary studies may include a confirmatory biopsy, PCR, and
electron microscopy.
Bacterial Infections 101
Bacterial Infections
Bacterial Vaginosis
Microbiology
●● BV is a polymicrobial infection associated with overgrowth of
several anaerobic bacteria including mainly Gardnerella vagina-
lis, but also Mobiluncus spp., Mycoplasma hominis, Prevotella
spp., Bacteroides spp., Ureaplasma spp., and Peptostreptococ-
cus spp.
●● These bacteria overgrow the lactobacilli, raising the vaginal pH
and produce malodorous amines.
●● BV is a risk factor for HPV infection acquisition. Women with
HPV-induced abnormalities in Pap tests have a higher propor-
tion of clue cells than their HPV-negative counterparts. The
exact association between BV and CIN development is unclear
(Fig. 5.10).
Fig. 5.10. Shift in vaginal flora. (Left) Conventional Pap smear show-
ing altered vaginal flora. The large number of bacteria in this specimen
imparts a gray color to the background smear (Pap stain, intermedi-
ate magnification). (Right) Clue cells are shown with squamous cells
coated by many small coccobacillary bacteria (Pap stain, ThinPrep,
high magnification).
Clinical Features
●● Infection in women of any age can be asymptomatic or patients
may present with a vaginal discharge or offensive (fishy) odor.
Clinical (Amsel) criteria for the diagnosis include vaginal
pH ³ 4.7, homogeneous milk-like discharge, amine “fishy” odor,
and clue cells in a wet mount.
●● Gynecologic sequelae of BV may include increased frequency
of pelvic inflammatory disease (PID) and posthysterectomy
vaginal cuff cellulitis.
●● In pregnant women, BV can result in preterm labor, chorioamnio-
nitis, premature rupture of membranes, postpartum endometritis,
and low birth weight in newborns.
●● The characteristic finding is the presence of coccobacilli coating
squamous cells imparting a grainy look to the cell (so-called “clue
cells”). The adherence pattern of these bacteria to squamous cells
between conventional smears and liquid-based Pap tests is similar.
●● Coccobacilli may also form a film pattern in the background,
best seen in conventional smears. In liquid samples, the back-
ground may be clean or bacteria are more clumped.
●● Many erythrocytes may be observed attached to clue cells.
●● Lactobacilli are absent.
●● Background inflammation is variable but usually sparse.
●● Epithelial cells may have inflammatory and reactive changes.
Diagnostic Note
●● The Bethesda system interpretation is “shift in flora suggestive
of bacterial vaginosis.” The reason is that the detection of coc-
cobacilli does not necessarily indicate clinical infection of BV.
●● The presence of at least 20% clue cells on a cervical Pap test
appears to be an accurate and reproducible criterion for the diag-
nosis of BV.
Ancillary Tests
●● Although rarely used by cytologists, the “whiff test” can be per-
formed at the bedside, whereby volatile amines are liberated when
vaginal secretions are mixed with 10% potassium hydroxide.
●● Gram stain
●● Culture
●● Multiplex PCR for both G. vaginalis and Mobiluncus spp.
Neisseria gonorrheae
Microbiology
●● Neisseria gonorrheae is a sexually transmitted infection.
●● They are Gram-negative diplococci, typically found within neu-
trophils.
Clinical Features
●● Infected patients are often asymptomatic, but may present with
pruritis, a mucopurulent vaginal discharge, dysuria, and edema-
tous, friable cervix.
●● If untreated, urethritis, endometritis, tubo-ovarian abscess, and
PID may develop. Scarring from PID may result in infertility or
ectopic pregnancy. Disseminated disease is possible.
●● Monococci or diplococci may be seen within neutrophils. How-
ever, cytolomorphology alone is not a reliable diagnostic modal-
ity and ancillary tests are required.
●● Patients with chronic gonorrhea infection may show reactive
epithelial change.
Diagnostic Note
●● Many women are routinely screened for N. gonorrheae infec-
tion, along with C. trachomatis at the time of Pap test collection.
Concomitant testing for these microorganisms does not appear
to affect the adequacy of the Pap test, even if separate endocer-
vical swabs are obtained before or after the Pap test. The type
of collection device (e.g., broom, brush) also does not appear to
impact the test.
●● Nucleic acid amplification tests (NAATs, see below) permit test-
ing of female patients to be performed on endocervical swabs,
liquid-based Pap specimens, self-collected vaginal swabs, and
urine specimens.
Ancillary Tests
●● Gram stain.
●● DNA for N. gonorrheae can be performed on liquid-based cytol-
ogy of cervicovaginal specimens. Commercial kits are available
that employ NAAT. These offer more rapid results than culture.
Second-generation assays (e.g., APTIMA Combo 2 assay) can
simultaneously detect N. gonorrheae and C. trachomatis from
the same specimen.
●● Culture, which needs to be performed within 24 h or less of
specimen collection.
●● Also available are fluorescent antibody testing, co-agglutination,
and DNA probe.
Actinomyces
Microbiology
●● Actinomyces spp. are Gram-positive, nonacid-fast bacte-
ria that exhibit branching, filamentous growth. Actinomy-
ces israelii is the species most commonly associated with
the female genital tract. They are part of the normal flora of
the mouth and gastrointestinal tract, and less commonly the
vagina. Damage to the mucosa is required for the develop-
ment of actinomycosis.
●● Actinomyces spp. grow as colonies that can form abscesses and
subsequent fibrosis. Yellow sulfur granules containing bacteria
may be visible macroscopically.
●● Actinomyces infection of the female genital tract is most often
associated with intra-uterine contraceptive device (IUD) use.
Around 25% of patients with an IUD will have Actinomyces
present in their Pap test specimens. Rare cases may develop
endometritis and/or PID.
Clinical Features
●● Symptoms may include vaginal bleeding and discharge, fever,
weight loss, and abdominal pain. Patients may present with a
tubo-ovarian abscess (Fig. 5.11).
Fig. 5.11. Actinomyces. (Left) Conventional Pap smear showing dense

balls of bacteria with radiating filaments consistent with Actinomyces spp.
(Pap stain, high magnification). (Right) ThinPrep Pap test showing a ball
of Actinomyces organisms (Pap stain, high magnification).
●● The main finding is dense basophilic balls (“dust bunnies”) of
bacteria with radiating filaments. Their center is often more
dense and poorly stained than the surrounding delicate fila-
ments (best visualized by focusing up and down). Occasionally
the organisms may be arranged in a horizontal array. At higher
magnification the filaments may be club-shaped and can be seen
branching at acute angles.
●● In conventional Pap smears bacteria balls are gray-blue in color,
whereas with liquid-based specimens they may be more eosi-
nophilic.
●● Acute inflammatory cells are often present in the background,
as well as macrophages, rare multinucleated giant cells and cal-
cified debris, the latter of which is probably from the IUD.
Diagnostic Note
●● The Bethesda system interpretation is “Bacteria morphologi-
cally consistent with Actinomyces spp.”
●● IUD removal and possible antibiotic treatment may be required
in symptomatic patients if actinomycosis is diagnosed.
Ancillary Tests
●● Gram stain
●● Culture
Granuloma Venereum
●● This STD, also known as granuloma inguinale and Donovano-
sis, is caused by Klebsiella granulomatis, an intracellular Gram-
negative bacteria, sometimes referred to as a Donovan body.
●● The organism is seen in histiocytes, enclosed within thin-walled
intracytoplasmic vacuoles. The classic “safety-pin” appearance
of the bacteria is not apparent in alcohol-fixed smears.
●● There may be a paucity of epithelial cells present due to ulceration.
As a result, the majority of the Pap test is comprised of inflamma-
tory cells, mainly neutrophils but also macrophages. Epithelioid
histiocytes may be encountered, but giant cells are not seen. Intact
capillaries may be seen due to direct scraping of the stroma.
●● Various ancillary tests are available including special stains
(Romanowsky and Warthin-Starry stains), immunocytochemis-
try, PCR, serology, culture, and electron microscopy (Fig. 5.12).
Tuberculosis
Microbiology
●● Tuberculosis (TB) of the female genital tract is primarily caused
by Mycobacterium tuberculosis.
●● TB involvement of the female genital tract in almost all cases
is secondary to extragenital disease, and usually involves the
fallopian tubes and endometrium. Infection of the cervix is rare,
even where mycobacterial infection is endemic.
●● The cervix is infected through direct spread from the upper gen-
ital tract or lymphatic spread. It has been suggested that occa-
sionally cervical TB may be sexually transmitted from a partner
with tuberculous epididymitis or if infected sputum is used as a
sexual lubricant.
Clinical Features
●● Patients may present with amenorrhea, menstrual irregularities,
infertility, vaginal discharge, and postmenopausal bleeding. The
Fig. 5.12. Donovanosis (high magnification images). (Left) A cervical

smear showing many macrophages containing intracellular organisms
present in a background of predominantly acute inflammatory cells (Pap
stain). (Top right) Conventional Pap smear showing macrophages contain-
ing bacteria scattered among benign squamous cells (Pap stain). (Bottom
right) Epithelioid macrophage with intracytoplasmic vacuoles containing
many Donovan bodies (Pap stain) (images courtesy of Prof. Gladwyn Lei-
man, University of Vermont, USA).
gross appearance of the tuberculous cervix is highly variable

(e.g., ulcer, polyp).
●● Cases of TB cervicitis are often clinically misdiagnosed as car-
cinoma of the cervix.
●● The main finding is granulomatous inflammation with or with-
out necrosis. Epithelioid histiocytes form sheets or can be seen
as single cells, along with acute and chronic inflammatory cells
in the background, as well as multinucleated giant cells.
Diagnostic Note
●● The presence of granulomas with multinucleated giant cells in
Pap tests should raise the suspicion of tuberculosis.
●● Granulomas in Pap tests can also be seen in other conditions
such as syphilis, granuloma inguinale, amebiasis, schistosomia-
sis, foreign body (suture) granulomas, and malakoplakia.
Ancillary Tests
●● Acid-fast stains for mycobacteria
●● Autofluorescence
●● Culture
●● PCR
Chlamydia trachomatis
Microbiology
●● Chlamydia (previously called TRIC agent) are obligate intrac-
ellular Gram-negative bacteria. They require growing cells to
remain viable, forming intracellular inclusions as they grow.
●● C. trachomatis is transmitted via sexual contact and during vag-
inal child birth. This is the most common nonulcerative STD
worldwide. Coinfection with HPV, gonorrhea, syphilis, HSV-2,
and HIV is common (Fig. 5.13).
Fig. 5.13. Chlamydia inclusions. (Left) Squamous cells on a Pap test are
shown with several small intracytoplasmic chlamydia inclusions (Pap stain,
high magnification). (Right) Squamous cell with a nebular body, which is
highly specific for chlamydial infection (Pap stain, high magnification).
Clinical Features
●● Most infected patients are asymptomatic.
●● Female urogenital infection may cause vaginal bleeding, dis-
charge, pelvic pain, dyspareunia, and urinary symptoms. Patients
develop cervicitis (typically follicular type), and possibly salp-
ingitis, PID, and/or Reiter’s syndrome (genital inflammation
with conjunctivitis and arthritis).
●● Chlamydia may also result in ophthalmic infection (trachoma)
and systemic disease.
●● Inclusion bodies may be seen in squamous, endocervical, and/
or metaplastic cells. Several different types of inclusions have
been described including small elementary bodies, larger reticu-
late bodies, and aggregate bodies (e.g., nebular body).
●● Reactive cellular changes may include cytomegaly, nuclear
enlargement, nuclear irregularity, and multinucleation.
●● Mixed acute and chronic inflammatory cells are often present.
Diagnostic Note
●● The interpretation of Chlamydia is not included in the Bethesda
System, because of the low sensitivity and reproducibility of
cytologic findings and the availability of more specific detection
methods.
●● The finding of intracellular inclusions within epithelial cells is
not diagnostic of chlamydia infection, as there are many other
causes for such vacuoles (faux chlamydia inclusions) including
intracellular targetoid mucin, condensed secretions, intracellu-
lar debris, degeneration, IUD effect, and radiation change. Mac-
rophages may also show a similar vacuolated appearance.
Ancillary Tests
●● Giemsa stain demonstrates chlamydial organisms
●● NAAT, which facilitates screening. Swabs and liquid-based
samples are both acceptable. Commercial assays (e.g., APTIMA
Combo 2 assay) can simultaneously detect N. gonorrheae (GC)
and C. trachomatis (CT) from the same liquid-based cytology
specimen. Nucleic acid testing cannot differentiate dead from
viable organisms.
●● Other nucleic acid tests (e.g., PCR, transcription-mediated amplifi-

cation, strand displacement amplification, ligase chain reaction).
●● Immunocytochemistry.
●● Antigen detection (direct immunofluorescence and ELISA).
●● Serology, which is of limited value in adults. Detection of IgM
in neonatal infection is useful.
●● Culture using susceptible cells (e.g., McCoy cells). Culture is
the test of choice (gold standard) in sexual abuse cases.
Fungal Infections
Candida
Microbiology
●● Candida may be identified in the vaginal tract of up to 50% of
asymptomatic women.
●● Candida albicans is seen in most (90%) infections (called candi-
diasis or candidosis). Less common causes are Candida glabrata
(previously called Torulopsis glabrata) forms small budding
yeasts, but not pseudohyphae and Candida parapsilosis.
●● Pregnancy, diabetes, and immunosuppression predispose women
to the development of candidiasis.
●● Candida vulvovaginitis is not considered to be an STD, and
appears not to be associated with an increased risk of SIL.
Clinical Features
●● Infection can be asymptomatic or patients with vulvovaginitis
may experience pruritis, burning, or have a yellow-white thick
(“cheesy”) discharge.
Cytolomorphogic Features
●● Budding yeasts and/or pseudohyphae are noted (“sticks and
stones” or “spaghetti and meatballs”). Yeast are 3–7 mm in size,
round to oval, and sharply defined. Pseudohyphae are formed by
budding, have parallel side walls, and show constriction along
their length (like a string of sausages).
Fungal Infections 111
Fig. 5.14. Candida. (Left) Candida hyphae in this ThinPrep Pap test
appear to have skewered the surrounding squamous cells forming a shish
kebab-like structure (Pap stain, intermediate magnification). (Right)
Higher magnification shows characteristic pseudohyphae with distinct
constrictions along their length (Pap stain).
●● C. glabrata presents with budding yeast only. The yeasts are

often surrounded by halos and may cluster.
●● Fungal elements may appear to “skewer” surrounding squamous
cells (making “shish kebabs”).
●● Candida-associated nonspecific changes that may be observed
in squamous cells include perinuclear halos, keratotic change
(intense orangeophilia and anucleate squames), and vacuolated
(“moth-eaten”) cytoplasm (Figs. 5.14 and 5.15).
Diagnostic Note
●● The Bethesda System recommends reporting these organisms
as “Fungal organisms morphologically consistent with Can-
dida spp.”
●● The identification of Candida on a Pap test does not necessarily
indicate infection.
●● Nonspecific reactive changes in squamous cells may be inter-
preted as ASC-US or pseudokoilocytosis. True dysplastic cells
have larger and more hyperchromatic nuclei.
Fig. 5.15. Candida glabrata. With C. glabrata the only finding in a Pap test
is rare to many yeasts (left and right images Pap stain, high magnification).
●● The diagnosis of well-formed pseudohyphae and/or spores is

needed to make a diagnosis of Candida. Other fungi like Geot-
richum, which have true hyphae and contaminating fibers, are
included in the differential.
Ancillary Tests
●● Special stains (PAS and GMS)
●● Fungal culture
Parasitic Infections
Trichomonas vaginalis
Microbiology
●● Trichomonas vaginalis is a parasitic protozoan that causes tri-
chomonaisis.
●● Trichomoniasis is a very common sexually transmitted infec-
tion. Its prevalence is highest among those with multiple sexual
partners and other sexually transmitted infections (Fig. 5.16).
Parasitic Infections 113
Fig. 5.16. Trichomoniasis. (Left). Many pear-shaped blue-gray trichomon-

ads are shown attached to a squamous cell in a ThinPrep Pap test (Pap stain,
high magnification). (Upper right) Several trichomonads are shown in this
conventional Pap smear with prominent red cytoplasmic granules (Pap
stain, high magnification). (Middle bottom) A darker gray elliptical nucleus
can be seen within these protozoa (high magnification under oil). (Bottom
right) Trichomonads demonstrate p16 immunoreactivity. Note the thin flag-
ella of the parasite on the right (immunocytochemistry, clone G175-405,
BD Biosciences Pharmingen, San Diego, CA; oil magnification).
Clinical Features
●● Patients may be asymptomatic or present with burning, pruri-
tis, a profuse yellow-green, frothy and malodorous vaginal dis-
charge and dysuria. Males may present with urethritis.
●● Trichomonas may be associated with PID, infertility, and in preg-
nant women premature rupture of membranes and preterm birth.
●● Round to oval or pear-shaped extracellular organisms are seen
usually just slightly larger than inflammatory cells and paraba-
sal cells. They range in size from 15 to 30 mm. In liquid-based
preparations the organisms are often smaller due to rounding. On
Pap stain their cytoplasm is gray and red cytoplasmic granules

may be noted. The nucleus is eccentrically situated and appears
a darker gray than the cytoplasm, but is still pale and vesicular.
Flagella are not usually seen on conventional smears, but may
be noted in liquid-based preparations.
●● Trichomonads may be present singly or aggregate in small colo-
nies (“Trich parties”) scattered around the slide. They may also
attach in large numbers to squamous cells.
●● Leptothrix may be associated with Trichomonas.
●● Associated inflammatory reactive changes (“Trich change”)
include neutrophils present in ball-like arrangements (poly can-
nonballs), squamous cells with small perinuclear (trich) halos,
mild nuclear hyperchromasia, slight nuclear enlargement,
pseudokeratinization, increased numbers of anucleate (ghost)
squames, erythrophagocytosis by trichomonads, and dirty
background.
Diagnostic Note
●● Diagnosis made by the identification of trichomonads on wet
mount preparation and Pap test has lower sensitivity (50–80%)
compared to culture (70–100%).
●● The morphologic identification of T. vaginalis on a Pap test is
highly accurate and should not require confirmatory testing.
●● Degenerated inflammatory cells, cellular debris, degenerated
bare epithelial nuclei in atrophic vaginitis, and small mucus
aggregates may be confused with trichomonads. Trichomonads
by comparison have a well-defined shape and a gray eccentri-
cally located nucleus.
Ancillary Tests
●● Immunocytochemistry. With the p16 immunostain (using clone
G175-405 from BD Biosciences Pharmingen, San Diego, CA,
USA) nonspecific immunoreactivity of T. vaginalis has been
reported.
●● Immunofluorescent antibody staining
●● PCR
●● Culture
Fig. 5.17. Schistosomiasis. (Left) Several nonviable empty ova of S. hae-

matobium are shown in a conventional Pap smear with a bloody back-
ground (Pap stain, high magnification). (Right) A miracidium (upper
structure) and ovum (lower structure) of S. haematobium in a Pap smear
are shown. The miracidium has possibly just escaped from the ovum (Pap
Schistosomiasis
Microbiology
●● Schistosomiasis is due to infection by the trematodes (flukes)
Schistosoma haematobium, S. mansoni, or S. japonicum. Cervi-
cal infections are most often due to S. haematobium.
●● Mature ova release miracidia in moist environments. The cervix
is sufficiently moist to allow this (Fig. 5.17).
Clinical Features
●● Cervical symptoms of infection include vaginal discharge and
bleeding. The infected cervix appears inflamed, ulcerated, nod-
ular, and friable, which may mimic carcinoma clinically.
●● Early infection causes inflammation (eosinophils, lymphocytes,

and granulomas) around ova. Chronic inactive infection with
calcified dead eggs leads to scarring.
●● The relationship between schistosomiasis and cervical cancer is
unclear. It is postulated that cervical schistosomiasis damages
cervical epithelium, thereby serving as a co-factor for the trans-
mission of viral infections such as HIV and HPV infections in
endemic regions.
●● Viable ova are 150 mm in length and 50 mm in width and are sur-
rounded by a thick shell. S. haematobium has a terminal spine
while S. mansoni has a lateral one. S. japonicum is slightly oval
with a rudimentary lateral spine. Sometimes the structure of a
miracidium within the ovum is apparent.
●● Nonviable ova are empty (have no internal structure) and may
exhibit a variety of forms including calcified, black, opaque,
shrunken, or collapsed eggs. Empty shells are often found in
association with multinucleated histiocytes.
●● Miracidia are not often seen. They usually have a pointed ante-
rior end and round posterior end. Cilia are not seen on Pap
smear. The cytoplasm containing various structures within
the miracidia stain brightly eosinophilic while the nuclei are
basophilic.
●● There is usually an acute inflammatory infiltrate and multinu-
cleated histiocytes present in the background.
Diagnostic Note
●● Cervical infection may occur in the absence of urinary egg
excretion.
●● The differential diagnosis for empty ova includes collections of
lubricant gel and plant cells. Lubricant gel lacks a spine and
is not refractile while plant cells may be refractile but lack a
spine.
●● Viable ova appear different from the ova of other parasites that
have been described in cervical smears including Ascaris, Tri-
churis, Enterobius, and Taenia. Refer to parasitic ova in Chap. 4.
●● Miracidia are larger than those of Balantidium coli.
Ancillary Tests
●● Special stains include GMS and Ziehl-Neelsen
●● Serology
Enterobius vermicularis
Microbiology
●● Enterobius vermicularis (known as the pinworm or thread-
worm) is an intestinal parasite (nematode) that can occasionally
migrate to the vagina, uterus, and even the peritoneal cavity via
the fallopian tubes.
●● The finding of an adult pinworm and/or egg on a Pap test
slide likely represents contamination from perianal parasites
(gravid female worms and ova), or infrequently a true genital
infection.
Clinical Features
●● Symptoms of intestinal infection (enterobiasis) mainly include
perianal pruritis.
●● Vaginal discharge may occur with infestation of the lower
genital tract.
●● An Enterobius ovum is oval, measures 50–60 × 20–30 mm in
size, and has a thick double-walled shell that is flattened on one
side. Occasionally, larvae may be seen in the ova or free-lying.
One may find one or many ova in a Pap test specimen.
●● The adult pinworm is cylindrical and has a sharply pointed pos-
terior end. Female worms measure 8–13 mm long and males are
only 2–5 mm in length. Both are ~0.5 mm thick.
●● With contamination there will be no associated inflammation.
With a true genital infection the background inflammatory
response varies and includes granulomatous inflammation.
Diagnostic Note
●● Psammoma bodies and pollen grain may mimic parasitic ova.
Fig. 5.18. Enterobius vermicularis (Left) pinworm egg seen in a conven-

tional pap smear, which is flat on one end (pap stain, high magnification)
(courtesy of Dr. Gladwyn Leiman, University of Vermont, USA). (Right)
Pinworm egg shown in cell block material from a cervicovaginal speci-
men (H&E stain, high magnification).
●● Enterobius ova need to be distinguished from Ascaris, Trichuris,

and Taenia eggs.
●● Plant and synthetic fibers may mimic pinworms.
●● The Strongyloides stercoralis adult worm is 180–350 mm
long, also has a curved pointed tail, but one can often also
find a short buccal canal. Microfilariae can be distinguished
because they have a sheath and contain many nuclei along
their length.
Ancillary Tests
●● Microbiology consultation
●● Examination of stool for parasites and/or cellulose (Scotch/
sticky) tape applied to the perianal skin for microscopic exami-
nation (Fig. 5.18).
Insects 119
Insects
Phthirus pubis
●● Phthirus pubis, also known as pubic or crab lice, are wingless
parasitic insects usually found on pubic hair, but may also be
seen on other hairy parts of the body including the eyelashes.
●● Lice have three distinct body segments, in addition to crab-like
claws on the legs for climbing hairs. They have an overall “crab-
like” appearance. They measure between 1 and 2.5 mm in size.
●● The presence of a pubic louse on a Pap test represents a contam-
inant. The clinician should be alerted to the possible infestation
of the pubic hair.
●● Pediculus humanus capitis (head lice) and Pediculus humanus
human (body lice) are morphologically distinct (Fig. 5.19).
Fig. 5.19. Phthirus pubis seen on a conventional Pap smear (Pap stain,
medium magnification).
Suggested Reading
Aslan DL, McKeon DM, Stelow EB, Gulbahce HE, Kjeldahl K, Pambuccian
SE. The diagnosis of trichomonas vaginalis in liquid-based Pap tests:
morphological characteristics. Diagn Cytopathol. 2005;32:253–9.
Discacciati M, Simoes J, Amaral R, Brolazo E, Rabelo-Santos S, Westin
M, et al. Presence of 20% or more clue cells: an accurate criterion for
the diagnosis of bacterial vaginosis in Papanicolaou cervical smears.
Diagn Cytopathol. 2006;34:272–6.
Giacomini G. Permanent diagnosis of bacterial vaginosis: gram stain or
Papanicolaou stain? Diagn Cytopathol. 2000;23:292–3.
Gupta R, Dey P, Jain V, Gupta N. Cervical tuberculosis detection in
Papanicolaou-stained smear: case report with review of literature.
Diagn Cytopathol. 2009;37:592–5.
Huang JC, Naylor B. Cytomegalovirus infection of the cervix detected
by cytology and histology: a report of five cases. Cytopathology. 1993;
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granuloma inguinale. Diagn Cytopathol. 1986;2:138–43.
McMillan A. The detection of genital tract infection by Papanicolaou-
stained tests. Cytopathology. 2006;17:317–22.
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chomonas vaginalis in liquid-based cytology. Acta Cytol. 2010;54:582–6.
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nalis p16 immunoreactivity in cervicovaginal Pap tests: a diagnostic
pitfall. Diagn Cytopathol. 2005;33:210–3.
Tambouret R. Gynecologic infections. In: Kradin RL, editor. Diagnostic
pathology of infectious disease. Philadelphia: Saunders Elsevier; 2010.
p. 443–63.
6
Pulmonary Infections
Walid E. Khalbuss1, Rodolfo Laucirica2,
1
2
Department of Pathology and Immunology, Baylor College of Medicine,
Ben Taub General Hospital, Houston, TX, USA
The lungs are a frequent site of infectious diseases. An accurate

diagnosis of infection by means of cytology can be lifesaving.
Sputum, lung FNA, bronchoscopic brushing, washing, and BAL
are useful procedures that can help provide a fast, cost-effective,
and noninvasive diagnosis of pulmonary infection. Pleuropulmo-
nary infections include bronchitis and bronchiolitis, pneumonia
(inflammation of the lung parenchyma), lung abscess, cavity for-
mation, allergic bronchopulmonary reaction, as well as pleural
effusion and empyema (pus in the pleural cavity).
A variety of microorganisms can infect the lungs including
viruses, bacteria, fungi, and parasites. The implicated pathogen
depends in part on the clinical setting. For example, microorgan-
isms responsible for community-acquired pneumonia include
Streptococcus pneumoniae, Haemophilus influenzae, and Staphylo-
coccus aureus. Atypical community-acquired pneumonia is caused
by Mycoplasma pneumoniae, Chlamydia spp. and several viruses
including respiratory syncytial virus (RSV) and parainfluenza virus
in children and influenza A and B in adults. Nosocomial infections
may be caused by Klebsiella spp., Escherichia coli, Pseudomonas
spp., and penicillin resistant S. aureus. Finally, there are certain
pathogens responsible for infections in the immunocompromised
host like cytomegalovirus (CMV), Pneumocystis jirovecii, and
Mycobacterium avium-intracellulare (MAI). This chapter discusses

122 6. Pulmonary Infections
the cytologic features of a variety of pathogens that infect the

respiratory tract.
The optimal diagnostic method depends on the location of the
lesion and radiologic findings. Sputum samples, and bronchial
brushings and washings yield diagnostic material for centrally
located lesions that involve major airways, while a BAL is useful
for assessing inflammatory and infectious processes in the periph-
eral regions of the lung. Transbronchial or ultrasound guided FNA
permits endobronchial lesions or hilar lymph nodes to be sampled,
and radiologically guided FNA is used when subpleural regions
need to be aspirated that cannot be assessed by bronchoscopy.
Given that cytologic examination of the respiratory tract is less
invasive compared to open surgical biopsies, cytology is often the
initial and only means by which patients are evaluated for infec-
tious diseases. This is especially true in immunocompromised
patients who need to be followed over a given period of time to
rule out opportunistic infections. In fact, BAL remains the diag-
nostic procedure of choice for detecting opportunistic infections in
immunocompromised hosts.
Viral Infections
Viruses are one of the most common causes of infection of the
respiratory tract. Not all viral infections have cytopathic changes
(e.g., influenza, swine flu, severe acute respiratory syndrome/
SARS, EBV). However, in many cases the cytologic features of
viral infection are fairly specific as to the etiology (Table 6.1).
Ancillary studies such as immunohistochemistry, viral culture, and
molecular tests are often necessary to accurately identify the cause
of certain infections.

Microbiology
●● Herpesvirus types 1 and 2 (HSV 1 and 2) can both infect the
lungs.
Viral Infections 123
Table 6.1. Cytologic featuwres of common pulmonary viral pathogens.

Virus Cytologic finding
Herpes simplex / herpes zoster virus Cowdry type A and B inclusions
Cytomegalovirus Large intranuclear and small cytoplasmic
inclusions
Adenovirus Intranuclear inclusions (smudge cells)
and ciliocytophthoria
Respiratory syncytial virus Syncytial giant cells
Parainfluenza Syncytial giant cells with large cytoplasmic
inclusions and ciliocytophthoria
Measles Multinucleated giant cells with cytoplasmic
and intranuclear Cowdry type A inclusions
Clinical Features
●● HSV infection of the upper respiratory tract can lead to pharyn-
gitis, laryngotracheitis, and pneumonia. HSV infection of the
lung may cause a necrotizing pneumonia or diffuse interstitial
pneumonia.
●● HSV commonly infects neonates and immunocompromised
patients.
●● Herpetic inclusions can be found within metaplastic squamous
cells when the inflammation is centered around airways or in
multinucleated giant cells within necroinflammatory debris in
the interstitial form of disease.
●● Infected cells often display prominent nuclear molding.
●● Two forms of characteristic herpes inclusions may be seen,
including Cowdry type A inclusions (distinct eosinophilic
intranuclear inclusions surrounded by a clear halo due to mar-
gination of chromatin material) and Cowdry type B inclusions
(eosinophilic ground glass “smudge nuclei” with margination of
the chromatin material) (Fig. 6.1).
●● The background may have associated acute inflammatory cells
and necrosis.
Fig. 6.1. BAL specimen from a patient with a history of colon adeno-
carcinoma who presented with respiratory distress. The left photos show
characteristic of Cowdry type B herpes inclusions. The right photo shows
accompanying reactive reparative change with prominent and multiple nucle-
oli that mimics malignancy in this case (Pap stain, high magnification).
●● Nonspecific reactive bronchial cells and alveolar macrophages
(multinucleated bronchial cells and cells with clearing/washed
out nuclei).
●● Squamous dysplasia in metaplastic cells or in a squamous papil-
loma lesion.
●● The cytopathic features are identical to those of herpes zoster
(clinical history and/or ancillary studies are required to resolve
this differential diagnosis).
●● CMV infection (rarely causes multinucleation, see Fig. 6.2 (see
next page)).
Ancillary Studies
●● Most cases do not need ancillary studies to confirm the
diagnosis.
Fig. 6.2. Co-infection with CMV and P. jirovecii is shown in this BAL
specimen from an immunocompromised patient. Characteristic “owl eye”
inclusions are seen. Multinucleation is rare in CMV infection, but can
occur (see inset). Pneumocystis infection resulted in the cast of frothy
material; each circlet with a central dot is an organism (Pap stain, interme-
diate magnification left and high magnification right).
●● Immunostains are available for HSV infection and can be

performed on cell block material or smears.
●● Viral culture.
●● HSV DNA detection by in situ hybridization or PCR.
●● Serology (type-specific assays).
●● Electron microscopy.
Microbiology
●● CMV is one of the most common causes of opportunistic infec-
tions involving the respiratory tract. In the respiratory tract, CMV
mainly targets pulmonary macrophages, endothelial cells and
fibroblasts, but virtually any cell can be infected by this virus.
Clinical Features
●● CMV pneumonia is frequently seen in patients with HIV/AIDS,
those receiving organ transplants, or individuals at the extremes
of age.
●● The diagnostic features of CMV infection include cytomegaly,
large amphophilic intranuclear inclusions with perinuclear halos
and chromatin margination (“owl eye” inclusion), and small
basophilic cytoplasmic inclusions.
●● The number of cells showing cytopathic changes varies with the
severity of infection or as a result of patients receiving prophy-
lactic antiviral therapy.
●● As CMV is frequently found in immunosuppressed patients, it
may be seen together with other opportunistic pathogens such as
fungi including P. jirovecii (Fig. 6.2).
●● Herpes simplex infection.
●● Neoplastic cells.
●● Reactive epithelial cells or macrophages with karyomegaly.
●● Other viral infections including adenovirus and RSV infection.
Ancillary Studies
●● Most cases do not need ancillary studies to confirm the diag-
nosis.
●● Immunocytochemistry or in situ hybridization for CMV.
●● Molecular testing (PCR).
Adenovirus
Microbiology
●● Adenovirus is a DNA virus that can cause ulcerative bronchiolitis,
acute pneumonia, or diffuse alveolar damage (DAD).
Fig. 6.3. Adenovirus pneumonia. The images on the left are of a smear
prepared from sputum showing an infected cell (circled) with a degenerated
nucleus (top left, Pap stain, intermediate magnification) and a detached cili-
ary tuft (bottom left, Pap stain, high magnification). The images on the right
are of a BAL from a child with adenovirus pneumonia showing a smudgy
appearing nucleus of an infected cell (top right, Pap stain, cytospin, high
magnification) with positive immunocytochemistry confirming this is due
to adenovirus infection (bottom right, high magnification) (BAL images
courtesy of Dr. S. Ranganathan, Pittsburgh Children’s Hospital, USA).
Clinical Features
●● Pulmonary adenovirus infections may occur in healthy subjects
living in close quarters (e.g., military recruits), but can also
cause severe and potentially fatal infections in immunocompro-
mised patients.
●● Infected cells exhibit two types of nuclear inclusions:
amphophilic intranuclear inclusions with perinuclear clearing
that mimic herpes simplex infection, or “smudge cells” where
large basophilic inclusions fill the entire nucleus and obscure
the chromatin detail (Fig. 6.3).
●● Another finding is the presence of decapitated ciliated respira-

tory epithelial cells, so-called ciliocytophthoria.
●● There may be an associated neutrophilic pneumonia, marked
hemorrhage, or evidence of necrosis.
●● Other viral infections such as herpes infection.
●● Reactive epithelial cells.
●● Cytotoxic drug injury.
Ancillary Studies
●● Immunocytochemistry for adenovirus.
●● Monoclonal antibody-based enzyme immunoassay can be
performed on a fresh specimen.
●● Immunofluorescence assay.
●● Microbiology tissue culture.
●● PCR.
●● Electron microscopy.
Respiratory Syncytial Virus (RSV)

Microbiology
●● RSV is an RNA virus (a member of the paramyxovidae subfamily
Pneumovirinae) that targets the respiratory lining epithelium.
●● Infection produces syncytial giant cells with inconspicuous
eosinophilic cytoplasmic inclusions.
Clinical Features
●● RSV is a major cause of lower respiratory tract infection
(bronchiolitis and pneumonia) during infancy and childhood.
●● RSV causes benign respiratory infections in older children
and has been linked to more severe adult community-acquired
pneumonia, acute bronchiolitis, and diffuse alveolar disease
(DAD) in the immunocompromised host or in lung allograft
recipients.
●● Syncytial giant cells with cytoplasmic inclusions surrounded by
clear halos.
●● Other viral infections such as human metapneumonia virus and
measles.
●● Benign noninfectious entities with giant cells.
Ancillary Studies
●● Binax NOW® RSV (BN) used on cytology specimens.
●● Microbiology tissue culture.
●● Shell vial culture.
●● PCR.
Parainfluenza
Microbiology
●● Human parainfluenza viruses are RNA viruses belonging to
the paramyxovidae family that cause upper respiratory tract
infections.
Clinical Features
●● In children, upper respiratory tract infections (e.g., croup) usually
follow a benign course.
●● Severe disease may occur in immunocompromised patients.
●● As with RSV, this infection is associated with syncytial giant
cells and epithelial cells with intracytoplasmic inclusions. How-
ever, these inclusions tend to be more frequent and larger than
those seen with RSV.
●● Ciliocytophthoria may be prominent.
●● Other viral infections such as RSV.
●● Benign noninfectious entities with giant cells (e.g., hard metal
pneumoconiosis).
Ancillary Studies
●● Immunocytochemistry for parainfluenza virus.
●● Rapid real-time multiplex PCR assay.
●● Multiplex nucleic acid sequence-based amplification (NASBA)
assay.
Measles
Microbiology
●● Measles (also known as rubeola) is an infection of the respi-
ratory system caused by the RNA rubeola virus of the genus
Morbillivirus.
●● Measles pneumonia is a rare and serious complication of the viral
exanthem, especially in immunocompromised patients.
Clinical Features
●● Measles pneumonia can range from mild (bronchiolitis) to
severe (DAD) disease.
●● Cytology specimens show large multinucleated giant cells with
cytoplasmic and intranuclear inclusions. The intranuclear inclu-
sion has a glassy, eosinophilic appearance reminiscent of Cowdry
types A inclusions (Fig. 6.4).
●● There may be associated acute inflammation.
●● Other viral infections such as RSV.
●● Benign noninfectious entities with giant cells morphology (e.g.,
hard metal pneumoconiosis).
Fig. 6.4. Measles pneumonia in a 42-year-old woman showing giant cell

pneumonia with enormous multinucleated giant cells that have cytoplas-
mic and intranuclear inclusions (Pap stain, high magnification). The inset
shows a cell stained with Phloxine Tartrazine that highlights the bright
red cytoplasmic inclusions (images courtesy of Dr. Pawel Schubert, South
Africa).
Ancillary Studies
●● Phloxine tartrazine special stain, which stains viral inclusions
bright red.
●● Serology: IgM (acute infection); IgG (immunity).
●● PCR (from a swab).
Bacterial Infections
Bacterial pneumonia may be lobar, lobular, or present in an atypi-
cal manner (e.g., mass-like or interstitial appearance). Gram-
positive and negative-bacteria are a common cause of pulmonary
infection. Most bacteria cause a nonspecific acute necroinflamma-

tory reaction associated with a variable fibrohistiocytic response
(organization). Necrotizing pyogenic infections may result in
abscess formation. Mycobacteria may evoke a granulomatous
process. The etiology of infectious pneumonia is best established
by correlating clinical and radiologic findings with microbiology
studies.
Actinomyces
Microbiology
●● Actinomyces are Gram-positive filamentous bacteria that cause
suppurative and granulomatous inflammation. Infections may
also result in bronchiectasis and abscesses containing sulfur
granules.
●● Pulmonary infections occur via aspiration of oral organisms and
are seen most often in persons with poor oral hygiene, immuno-
compromised patients, or from direct extension of cervicofacial
or subdiaphragmatic infection.
●● Secondary actinomycotic infection can involve devitalized lung
tissue damaged by other infections.
Clinical Features
●● The clinical manifestations of pulmonary actinomycosis are
fever, productive cough, and hemoptysis. Chronic infection may
cause sinus tracts.
●● Lung imaging findings may include consolidation, necrosis,
abscess, or an aspirated broncholith.
●● Specimens contain acute inflammation and bacterial colonies
composed of thin beaded and delicate branching filaments
that are cyanophilic with a Pap stain (so-called “cotton ball”
appearance).
●● Some cases may have sulfur granules which are colonies
of tangled Gram-positive bacilli, often coated with an eosi-
nophilic matrix of exudate plasma proteins (Splendore-Hoeppli

reaction).
●● Actinomyces are commonly found in tonsillar crypts, and
therefore may be seen (associated with squamous cells) con-
taminating sputum and bronchial specimens. Their presence on
FNA is unlikely to be due to contamination. True infection is
associated with abundant neutrophils.
●● Nocardia (less beading, no sulfur granules).
●● Botryomycosis (may also form sulfur granules, but contains
cocci).
●● Mycobacteria.
●● Fungal infection.
Ancillary Studies
●● Special stains (Actinomyces are positive with Gram and GMS
stains, but negative with an AFB/Fite stain).
●● Microbiology culture.
Nocardia
Microbiology
●● Nocardia are weakly staining Gram-positive, partially acid-fast,
rod-shaped, aerobic bacteria. They form beaded branching fila-
ments. The majority of infections (80%) are due to Nocardia
asteroides.
●● Pulmonary infection occurs via inhalation. Pre-existing pul-
monary disease, particularly pulmonary alveolar protienosis,
increases the risk of contracting Nocardia pneumonia.
Clinical Features
●● Patients commonly present with slowly progressive pneumo-
nia. In immuncompromised patients, infection may be associ-
ated with cavitary lung nodules. Infection can also spread to the
pleura or to chest wall.
Fig. 6.5. FNA of Nocardia pneumonia with numerous PMNs and necrotic
material (left image Pap stain, high magnification) associated with thin
filamentous branching bacteria (middle image Gram stain and right image
AFB stain, both high magnification).
●● Cytology findings include those of acute pneumonia (numerous
neutrophils and necrotic material) together with the presence
of thin filamentous, beaded bacteria with right angle branching
that resembles Chinese letters (Fig. 6.5).
●● Actinomyces (more beading and more commonly have sulfur
granules).
●● Mycobacteria.
Ancillary Studies
●● Special stains (Nocardia are positive with Gram and GMS
stains, and weakly positive with an AFB/Fite stain).
Tuberculosis
Microbiology
●● Pulmonary tuberculosis (TB) is caused by the bacterium Myco-
bacterium tuberculosis. Pulmonary TB may be due to primary
or reactivation (chronic) infection. Pulmonary manifestations of
TB include bronchopneumonia, caseating pneumonia, nodular
disease (tuberculoma), tracheobronchitis, milliary disease, hilar
lymphadenopathy, and pleural disease.
●● Individuals at risk for infection are those who are immunosup-
pressed, the elderly, and infants.
●● Nontuberculous mycobacteria (NTM), such as Mycobacterium
avium complex (MAC) and Mycobacterium kansasii, may also
cause pulmonary infections.
●● Infections are often associated with granulomatous inflammation.
In NTM infection, particularly in immunocompromised patients,
granulomas tend to be nonnecrotizing and incompletely formed.
Clinical Features
●● Patients usually present with night sweats, fever, weight loss,
fatigue, chronic cough, chest pain, hemoptysis, and possibly
extrapulmonary TB that may involve the pleura and mediastinal
lymph nodes.
●● Thoracic imaging studies may show infiltrates or cavities (espe-
cially of the upper lobes), solitary or milliary nodules, pleural
effusion, pneumothorax, and/or hilar lymphadenopathy.
●● The main finding is granulomas that show clusters of epithelioid
histiocytes that may be mixed with lymphocytes, Langhans, and/
or foreign body-type multinucleated giant cells with/without a
necrotic background (Fig. 6.6).
●● In NTM infections, macrophages laden with abundant myco-
bacteria may show abundant foamy cytoplasm (referred to as
pseudo-Gaucher cells).
●● A negative image of extracellular mycobacteria may be notable with
Diff-Quik, Giemsa, or other Romanowsky-type stains (Fig. 6.7).
In NTM infection, these unstained mycobacteria (especially within
macrophages) are usually more numerous.
Fig. 6.6. Necrotizing granulomatous pneumonia caused by M. tuberculosis
shown on Pap stained smears at high magnification (left and middle images)
and cell block (H&E stain, high magnification). Rare mycobacteria are seen
with an AFB stain (upper right image and inset, high magnification).
Fig. 6.7. Tuberculosis pneumonia with numerous mycobacteria seen as

negative images on Diff-Quik stain (high magnification).
●● Other microorganisms that cause necrotizing granulomatous
inflammation and are AFB positive (Nocardia, Rhodococcus,
and Legionella micdadei).
●● Noninfectious causes of granulomatous lung disease (e.g.,
sarcoidosis).
Ancillary Studies
●● Acid-fast stains (Ziehl-Neelsen or Kinyoun stains). The diag-
nosis of mycobacterial infection can be on the basis of the
identification of microorganisms with acid-fast (AFB) stains.
Mycobacteria with M. tuberculosis compared to NTM may be
rare and require careful and lengthy scrutiny of slides. Some
mycobacteria have a distinct morphology; for example M. kansasii
resembles a shepherd’s crook or candy cane and Mycobacterium
fortuitum closely resembles Nocardia spp.
●● Mycobacteria may be weakly Gram-positive and will stain with
GMS.
●● Fluorescence microscopy with fluorochrome dyes such as
auramine O or auramine–rhodamine are more sensitive and
specific than AFB stains.
●● Autofluorescence.
●● PCR for diagnosis and subclassification (can be done on cell
block material).
●● Culture for diagnosis and subclassification, although mycobac-
teria are slow growing and culture can take weeks (6–8 weeks
with conventional Lowenstein-Jensen medium and 3 weeks with
Middlebrook liquid and solid media).
Legionella
●● Pneumonia is the predominant manifestation of Legionella
infection (Legionnaire’s disease).
●● Bacteria (Gram-negative coccobacilli) can be identified with
silver stains (Steiner, Warthin-Starry, or Diertrle stains), and are
often abundant prior to therapy. Legionella micdadei stains with
modified Ziehl-Neelsen stains.
●● Immunocytochemistry (for Legionella pneumophilia) can be

performed if needed.
Fungal Infections
Pulmonary fungal infections can be readily diagnosed by means
of exfoliative cytology or FNA. Infections are often associated
with a granulomatous or necroinflammatory reaction. Fungal mor-
phology varies with the stage of the disease and fungal organism.
Table 6.2 summarizes the cytologic features of common fungal
pathogens that infect the respiratory tract.
Candidiasis
Microbiology
●● Candidiasis, infection caused by Candida spp., can involve the
lungs. Candida albicans is the primary causative agent. They
are yeast-like fungi that can form true hyphae and pseudohy-
phae.
●● Most cases of candida pneumonia are secondary to hematologi-
cal dissemination of organisms from a distant mucocutaneous
site.
●● The respiratory tract is often colonized with Candida spp.,
especially in hospitalized patients. Patients at particular risk of
Table 6.2. Morphology of pulmonary fungal organisms.

Species Morphology
Candida Pseudohyphae (elongated yeasts joined together)
Narrow neck “teardrop” shaped budding yeast (2–10 mm)
Histoplasma Narrow neck budding yeast (3–5 mm)
Blastomyces Broad neck budding yeast with a thick cell wall (5–15 mm)
Cryptococcus Yeast with thick capsules (5–20 mm)
Coccidioides Thick walled spherules (10–80 mm) filled with endospores
(2–5 mm)
Aspergillus Regular septate hyphae with 45° branching (3–6 mm wide)
Fruiting bodies (conidiophores)
Mucor Ribbon-like, nonseptate hyphae with 90° branching
(6–50 mm wide)
Fig. 6.8. Candidiasis in a BAL specimen with pseudohyphae (elongated

yeast joined together) and budding yeast (left Pap stain and right GMS
acquiring a candida lung infection include those with impaired

immunity (e.g., transplant recipients, HIV positive individuals,
those using corticosteroids, burn victims, and patients with a
hematologic neoplasm).
Clinical Features
●● Infection of the airways (laryngeal candidiasis and tracheobron-
chitis) may present with a sore throat, hoarseness, fever, produc-
tive cough, and possibly dyspnea. Candida pneumonia is usually
associated with disseminated candidiasis. The most common
form of infection is multiple lung abscesses.
●● Specimens containing candida elements may contain pseudo-
hyphae (elongated yeast joined together), true hyphae, and/or
budding yeast (blastoconidia) with/without background inflam-
matory cells (Fig. 6.8).
●● Contamination from oropharyngeal sites (e.g., oral thrush)
●● Other fungal organisms (e.g., Aspergillus, cryptococcus)
●● Fungal mimics (e.g., synthetic fibers, pollen grains, etc.)
Ancillary Studies
●● Fungal stains (GMS and PAS are positive)
●● Gram stain: Positive
Histoplasmosis
Microbiology
●● Histoplasmosis, caused by the dimorphic fungus Histoplasma
capsulatum, infection is acquired through inhalation of infective
spores (microconidia), which primarily target macrophages in
the respiratory system.
●● Pulmonary infection may be acute or chronic and present with
localized or diffuse pulmonary disease.
Clinical Features
●● Pulmonary histoplasmosis can present clinically with pneu-
monia, lung nodule, cavitary lung disease, mediastinal or hilar
lymphadenopathy, and even superior vena cava syndrome or
obstruction of other mediastinal structures.
●● It is not uncommon for localized infections to mimic cancer.
●● There are numerous intracellular yeasts measuring 3–5 mm, with
narrow based budding, within macrophages. When cells are
disrupted they may also be extracellularly located (Fig. 6.9).
●● Candida
●● Cryptococcus neoformans (microform)
Fig. 6.9. Histoplasmosis. (Left images) Macrophages are shown in this

ThinPrep specimen of a bronchoalveolar lavage specimen from an AIDS
patient with multiple intracellular yeast (Pap stain, top image intermediate
and bottom image high magnification). (Right images). Macrophages con-
taining H. capsulatum microorganisms are shown at high magnification in
these direct smears from lung specimens (Diff-Quik stain).
●● Blastomyces dermatitidis
●● P. jiroveci
●● Microcalcifications (especially in the cell block)
●● Platelets (extracellular only)
Ancillary Studies
●● Special stains (GMS and PAS stains are positive)
●● Antigen detection (enzyme immunoassay using urine, blood, or
bronchoalveolar lavage fluid).
●● Serology
Blastomycosis
Microbiology
●● This is a systemic infection caused by inhaling the conidia of the
dimorphic fungus B. dermatitidis.
●● Infections primarily involve the lung, usually associated with
the formation of microabscesses, but may disseminate to cause
extrapulmonary disease.
Clinical Features
●● Blastomycosis of the lung can be asymptomatic or manifest as
acute or chronic pneumonia. In the lungs, this organism usually
infects the upper lobes.
●● One finds round large yeast (5–15 mm) that have a character-
istic double contoured thick cell wall, and show broad-base
budding.
●● There is often associated granulomatous inflammation present.
●● Other fungal organisms (e.g., the microform of H. capsulatum
and giant form of Coccidioides immitis).
Ancillary Studies
●● Mucicarmine stain (negative, to exclude cryptococcus)
Cryptococcosis
Microbiology
●● Humans are infected with cryptococcus by inhaling basid-
iospores or yeast. The important human pathogens are Crypto-
coccus neoformans and Cryptococcus gattii.
●● The course of disease depends on whether yeast are encapsulated

(encapsulated yeast may cause a granulomatous reaction) and the
patient’s immune status. Invasive cryptococcus has become increas-
ingly common among HIV positive and transplant patients.
Clinical Features
●● Cryptococcal pulmonary disease varies from asymptomatic
airway colonization to a slowly progressive lung mass (cryp-
tococcoma), pneumonia, acute respiratory distress syndrome
(ARDS), and pleural effusion.
●● Round to oval yeasts measuring 5–20 mm are seen with narrow-
based buds.
●● Yeasts are surrounded by thick capsules that are positive with muci-
carmine, alcian blue, and colloidal iron stains (Figs. 6.10 and 6.11).
●● Other fungal organisms (e.g., candida, blastomycosis)
●● Fungal mimics
Ancillary Studies
●● Mucicarmine stain is positive in encapsulated forms
●● Fontana-Masson stain may stain the yeast wall
●● India ink (requires live organisms)
●● Serum cryptococcal antigen
Coccidioidomycosis
Microbiology
●● C. immitis infection typically causes a necrotizing granuloma-
tous inflammation. The major pulmonary manifestations include
Fig. 6.10. Cryptococcus pneumonia. Yeasts are round to oval and have
narrow-based buds (Pap stain left image, high magnification). Yeasts may
resemble pneumocystis cysts, but tend to be more variable and often larger
in size (left inset, DQ stain, high magnification). Encapsulated cryptococ-
cal organisms are surrounded by a thick capsule that stains with GMS (top
right), PAS (middle right), and mucicarmine (bottom right) stains (high
magnification).
pulmonary nodules, cavities, diffuse reticulonodular pneumo-

nia, and rarely pleural disease.
●● Fungemia can also produce multiple septic pulmonary emboli,
especially in patients with immune deficiency.
Clinical Features
●● Most people are asymptomatic following initial respiratory expo-
sure to arthroconidia. Those who become ill typically develop res-
piratory symptoms, such as cough, pleurisy, fever, and weight loss.
●● The common morphologic forms of C. immitis seen in
cytology specimens are thick walled spherules (measuring
Fig. 6.11. In cryptococcus pneumonia, organisms may be intracellular.

The halo around the organism indicates the presence of a thick capsule
(Pap stain, high magnification).
10–80 mm) that contain endospores (measuring 2–5 mm).

There are generally very few spherules present in most speci-
mens (Fig. 6.12).
●● Sometimes the spherules may be collapsed and appear as empty
structures, surrounded by scattered endospores all over the
slide.
●● Mycelial elements may rarely be present, but these have no dis-
tinguishing morphologic characteristics.
●● An inflammatory background with/without granulomas may be
present.
●● Other large fungal organisms (e.g., Rhinosporidium and Pro-
totheca wickerhamii).
●● Fungal mimics.
Fig. 6.12. Coccidioidomycosis. (Left images) The images shown on the

left are from a patient who presented with a lung mass that was thought
to be a malignancy. An intraoperative touch preparation (top left) revealed
a spherule with endospores (H&E stain, high magnification). The lung
resection in this case confirmed an infection due to Coccidioidomycosis.
A spherule is shown (bottom left) surrounded by granulomatous inflam-
mation and eosinophils (H&E stain, high magnification). (Right images)
The images on the right are from a lung FNA of a 33-year-old nonsmoking
man who presented with a 3 cm lung nodule. Present among the necrotic
acellular material were many large round spherules, some of which were
empty (top right) as they were disrupted after being smeared on the slide
(DQ stain, high magnification). A GMS stain in this case shows a spherule
filled with endospores and many dispersed free spores in the background
(high magnification).
Ancillary Studies
●● Fungal stains (GMS, PAS).
●● Gram stain is negative.
●● Mucicarmine stain is positive.
●● Wet preparation of fresh samples using saline or potassium
hydroxide solution can be utilized to demonstrate spherules.
●● Calcofluor staining is positive.
●● Immunocytochemistry using a specific fungal antibody

●● Serology and antigen tests
●● Skin test
Aspergillosis
Microbiology
●● Aspergillosis is caused by the fungus Aspergillus. Transmission
occurs via inhalation of airborne conidial forms.
●● Although most people are exposed to this fungus, infections
mainly occur in individuals with underlying lung disease (e.g.,
cystic fibrosis) or impaired immunity (e.g., transplant or AIDS
patients).
●● There are four types of lung disease caused by Aspergillus:
Allergic bronchopulmonary aspergillosis.
Aspergilloma (fungus ball or mycetoma), which develops in
a preexisting lung cavity.

Chronic necrotizing pneumonia.
Invasive pulmonary aspergillosis, which may cause lung inf-
arction and dissemination to other organs.
Clinical Features
●● Symptoms depend on the type of infection, and range from
cough to hemoptysis or manifestations from extrapulmonary
infection.
●● Chest imaging findings are also variable and may include pul-
monary infiltrates or a lung cavity with a fungus ball.
●● Usually only the hyphal form is seen, characterized by septate
hyphae with relatively straight walls and 45° (dichotomous)
branching (Fig. 6.13).
●● Conidial forms of this organism (fruiting bodies) are seen when
this organism is exposed to air (e.g., abscess cavity or involve-
ment of large airways).
Fig. 6.13. Aspergillosis shown in a ThinPrep preparation of a bronchial

washing. Hyphae have relatively straight walls with 45° (dichotomous)
branching. The hyphal form of the organism is also septated, best seen
with the GMS stain (right image, high magnification). A conidial form
(fruiting body) was observed in this specimen (left image, Pap stain, high
magnification), as well as calcium oxalate crystals (lower part of the middle
image, Pap stain, high magnification).
●● A necroinflammatory background is often present.

●● Calcium oxalate crystals, which are strongly birefringent
under polarized light, may be seen and are highly suggestive of
aspergillosis (Fig. 6.13).
●● Other fungal organisms (e.g., mucormycosis, candida, blasto-
mycosis).
Ancillary Studies
●● Fungal stains (GMS and PAS are positive).
Fig. 6.14. Pulmonary mucormycosis (zygomycosis). Sputum showing

terminal chlamydoconidia that are spherical and have thick walls (Pap
stain, intermediate magnification on the left, and high magnification for
right images).
●● Immunocytochemistry using an immunostain specific to the

Aspergillus genus (but not species specific).
●● Aspergillosis antibody test.
●● Galactomannan (a molecule from the fungus sometimes found
in blood).
●● Fungal culture.
Mucormycosis (Zygomycosis)
Microbiology
●● This invasive fungal infection is caused by mycelia-forming
fungi of the Mucorales (e.g., Rhizopus, Mucor spp.) and
Entomophthorales (e.g., Conidiobolus and Basidiobolus spp.)
orders.
●● Primary pulmonary zygomycosis tends to occur in patients with
immunosuppression such as patients with neutropenia, trans-
plant recipients, and in those persons receiving high-dose corti-
costeroid therapy (Fig. 6.14).
Clinical Features
●● Patients with pulmonary infection typically present with
respiratory symptoms like cough, hemoptysis, chest pain, and
dyspnea.
●● Specimens contain broad, ribbon-like, nonseptate, irregularly
shaped hyphae with right-angle branching.
●● One may only find a terminal chlamydoconidium that is spheri-
cal with thick walls.
●● A necroinflammatory background is often present.
●● Other fungal organisms (e.g., candida, blastomycosis).
Ancillary Studies
●● Fungal stains (GMS and PAS are positive).
●● Immunocytochemistry using a specific fungal antibody.
●● Direct immunofluorescence.
●● No serologic tests are available.
●● Fungal culture (3–5 days).
Pneumocystis
Microbiology
●● Pneumocystis pneumonia (or pneumocystosis) is caused by the
yeast-like fungus P. jirovecii (formerly called Pneumocystis
carinii).
●● Infection typically involves the distal airspaces and is associated
with a foamy or frothy exudate.
●● Immunocompromised patients including persons with AIDS
and those receiving immunosuppressive therapy are at increased
risk of infection.
Clinical Features
●● Symptoms include fever, nonproductive cough, shortness of
breath, weight loss, and night sweats.
●● Complications may include pneumothorax and extrapulmo-
nary disease. Pleural effusion and intrathoracic adenopathy are
rare.
●● Specimens used to diagnose pulmonary infection include spu-
tum (induced sputum is more sensitive than expectorated sam-
ples), BAL (more invasive but has a greater diagnostic yield),
and for intubated patients tracheal aspirates.
●● The typical finding is circumscribed foamy alveolar foamy casts
that contain cysts. In some cases, casts may be absent, with
organisms present only within macrophages.
●● The background inflammatory infiltrate is variable, and may
rarely include granulomas.
●● Organisms are not well stained but are still visible with a Papan-
icolaou stain, seen mainly as multiple clear spaces within casts.
Cysts are best visualized with silver stains (e.g., GMS).
●● Cysts measure 4–8 mm, resemble crushed ping-pong balls
(cup-shaped), and with a GMS stain a central dot-like area may
be seen representing a focus of cell membrane condensation
(Fig. 6.15).
●● Cysts tend to be present in aggregates of 2–8, and should not be
confused with Histoplasma or Cryptococcus which typically do
not aggregate.
●● Budding does not occur. However, adjacent or overlapping cysts
may mimic budding organisms.
●● Other fungal organisms (e.g., Candida, cryptococcus, blastomy-
cosis).
●● Alveolar proteinosis.
●● Amyloidosis.
●● Lysed red blood cells.
Fig. 6.15. P. jirovecii (carinii) seen in BAL ThinPrep specimens. Foamy

casts are shown containing “empty spaces” that represent cysts entrapped
in alveolar exudates (Pap stain, top left intermediate magnification, bottom
left high magnification). Numerous alveolar casts are also present in the
cell block (top right, H&E stain, intermediate magnification). The cysts
tend to aggregate together (bottom middle, GMS stain, high magnifica-
tion), and often have a central dot-like area in the cyst (right lower, GMS
●● Other potential mimics including mucus, lubricant, bacterial

clumps, talc, neutrophils, hemosiderin filled macrophages, and
epithelial cells.
Ancillary Studies
●● Cyst wall stains with GMS, PAS, and mucicarmine stains.
●● Intracystic or free sporozoites (not cyst walls) stain with Giemsa.
●● Immunocytochemistry using a specific Pneumocystis immuno
stain.
●● Calcofluor white.
●● Direct immunofluorescence.
●● PCR.
Table 6.3. Pulmonary parasitic organisms.

Protozoa
Toxoplasma gondii
Entamoeba histolytica
Cryptosporidium
Microsporidium
Nematoda (roundworms)
Dirofilaria immitis
Filaria spp. (Wuchereria bancrofti, Onchocerca volulus, etc.)
Strongyloides stercoralis
Cestoda (tapeworms)
Echinococcus granulosus, Echinococcus multilocularis
Trematoda (flukes)
Paragonimus spp. (westermani, africanus, mexicanus, etc.)
Schistosoma spp. (mansoni, japonicum, haematobium)
Parasitic Infections
Parasites are rare in most developed countries, but may be endemic
in other parts of the world. Pulmonary involvement often occurs
because the lungs represent a site of infection during the life cycle
of some parasites. Infection is often associated with eosinophilia
in the blood and pulmonary tissue. Table 6.3 lists parasitic organ-
isms likely to infect the respiratory tract.
Dirofilariasis
●● Humans may acquire Dirofilaria immitis (dog heartworm)
through insect vectors (mosquitoes) from dogs. Parasites that
become entrapped within pulmonary vessels may result in
pulmonary infarction.
●● FNA of infarcted nodules demonstrate worm fragments mixed
with necrotic lung tissue and an inflammatory and granuloma-
tous response.
●● Worms measure 120–310 mm in length depending on the sex
(females are larger than males). Dirofilaria are distinguished
from other nematodes by their prominent muscular lateral cords
and striated cuticle.
Fig. 6.16. Strongyloides stercoralis in a BAL specimen from an HIV

positive patient. The specimen shows many filariform larvae with rounded
ends and notched (coiled) tails (Pap stain, intermediate magnification left,
high magnification right).
Strongyloidiasis
●● Strongyloides stercoralis involves the respiratory tract via hema-
togenous spread of the infective form (filariform larvae), espe-
cially in those who are immunosuppressed.
●● Sputum, tracheal aspirates, and BAL samples are all useful for
establishing the diagnosis.
●● Filariform larvae are large (400–500 mm), and possess notched
tails and a short buccal cavity. They need to be distinguished
from the larval forms of Ascaris lumbricoides and hookworms
(Fig. 6.16).
Paragonimiasis
●● The species that commonly causes human infection is Parag-
onimus westermani.
Fig. 6.17. Paragonimus eggs identified in this FNA cell block from a lung
nodule. The eggs have a thick, double contour shell (H&E stain, low and
high magnification, left and right respectively).
●● Mature worms in the lung shed eggs that may be visible in

exfoliated samples (sputum or bronchial washings) or FNA
specimens.
●● Eggs have a thick, double contour shell with an operculated end
that has a flattened appearance, and, depending upon the species,
measure approximately 80–118 mm (Fig. 6.17).
Toxoplasma gondii
●● Lung involvement occurs with severe disseminated infection
(toxoplasmosis), especially in neonates (via congenital trans-
placental infection) and immunocompromised patients.
●● Respiratory specimens like BAL require close inspection for
crescent or arc-shaped free (extracellular) trophozoites, as they
measure only around 5–7 mm in length. Macrophages may be
seen containing several parasites. Parasites contain a prominent
Fig. 6.18. Toxoplasmosis in a BAL specimen from a transplant patient.

The extracellular trophozoites caught up in the mucus are banana-shaped
organisms with a prominent central nucleus (Giemsa stain, high magnifi-
cation). The parasites are barely visible with a Pap stain (right image, high
magnification). The inset in the middle shows an immunoreactive parasite
(immunocytochemical stain, high magnification).
central nucleus, and need to be distinguished from similar sized

Histoplasma (which exhibit narrow-neck budding) and Leish-
mania (which also contain a kinetoplast).
●● Parasitic organisms are best identified using a Giemsa-stained
preparation.
●● An immunohistochemical stain for Toxoplasma is available
(Fig. 6.18).
Entamoeba
●● With Entamoeba histolytica infection, the lungs may be involved
by extension from an amebic liver abscess or via hematogenous
spread.
Fig. 6.19. A sputum specimen from a 32-year-old man is shown with

E. gingivalis. The amebae are larger than histocytes, have amphophilic bub-
bly cytoplasm, and a sharply defined nuclear karyosome (Pap stains, inter-
mediate magnification on the left, high magnification middle and right).
●● E. gingivalis is a parasitic protozoan of the oral cavity. In patients

with poor oral hygiene, aspiration can result in a lung infection.
●● Amebae have a histiocyte-like morphology and typically con-
tain ingested RBCs in their cytoplasm. Trophozoites are, how-
ever, slightly larger than macrophages and have smaller nuclei
with coarser chromatin than histiocytes.
●● The morphologic appearances of E. histolytica and E. gingivalis
are quite similar, although the trophozoites of E. gingivalis tend
to be comparably larger (10–35 vs. 15–20 mm) and, unlike with
E. histolytica, there is no associated cyst stage. E. gingivalis is
also the only species of amebae that can phagocytose white and
red blood cells as well as ingest bacteria (Fig. 6.19).
Echinococcosis (Hydatid Disease)

●● The most common cestode pathologic to the lung is Echinococcus
granulosus, which manifests as an echinococcal (hydatid) cyst.
Fig. 6.20. Echinococcosis (hydatid disease of the lung). This lung FNA
from a 38-year-old woman yielded 20 mL of clear fluid that contained
numerous intact protoscoleces containing radially arranged hooklets
shown with a DQ stain (left, intermediate magnification) and Pap stain
(upper right, intermediate magnification). Detached hooklets resembling
shark’s teeth are also seen (DQ stain, lower right, high magnification)
(images courtesy of Dr. Pawel Schubert, South Africa).
●● Patients may be asymptomatic for many years. A primary

hydatid cyst of the chest may mimic a neoplasm.
●● FNA usually contains hydatid sand consisting of variable num-
bers of intact protoscoleces containing radially arranged hooklets
and detached (free) refractile hooklets (resembling shark’s teeth)
present in a background of thick granular material (Fig. 6.20).
●● Cell blocks may contain portions of a cyst wall that consists
of three layers: (1) host layer with giant cells, fibroblasts, and
eosinophils; (2) middle acellular laminated membrane; and
(3) inner germinal layer.
●● It is controversial whether suspected hydatid cysts should be
aspirated as fluid leakage could result in anaphylaxis or dis-
seminated disease.
Pleural Infections and Empyema

●● Pleural (parapneumonic) effusion occurs in 20–40% of hospital-
ized patients with bacterial pneumonia, and has three stages: exuda-
tive (early culture negative), fibrinopurulent (infected), and pleural
rind stage. Empyema is defined as pus in the pleural space.
●● Pleural infection can also occur following trauma, surgery,
esophageal rupture, or as a result of direct extension (from the
lung or subdiaphragmatic disease).
●● Infectious causes of pleural disease include bacteria (e.g., Strep-
tococcus, H. influenza, anaerobes, actinomycosis, Legionella),
mycobacteria, fungi (Candida, Pneumocystis), and parasites
(E. histolytica).
●● A predominance of neutrophils indicates an acute infection,
while many mononuclear inflammatory cells usually indicate a
more indolent process (e.g., TB or fungal infection).
●● Pleural fluid eosinophilia (>10%) may be caused by infection
(fungal, parasitic) and noninfectious causes (e.g., air, blood, drugs).
Suggested Reading
Lemos LB, Baliga M, Taylor BD, Cason ZJ, Lucia HL. Bronchoalveo-
lar lavage for diagnosis of fungal disease. Five years’ experience in a
southern United States rural area with many blastomycosis cases. Acta
Cytol. 1995;39:1101–11.
Moriarty AT, Darragh TM, Fatheree LA, Souers R, Wilbur DC. Perform-
ance of Candida – fungal-induced atypia and proficiency testing: obser-
vations from the College of American Pathologists proficiency testing
program. Arch Pathol Lab Med. 2009;133:1272–5.
Naimey GL, Wuerker RB. Comparison of histologic stains in the diagnosis
of Pneumocystis carinii. Acta Cytol. 1995;39:1124–7.
Pisani RJ, Wright AJ. Clinical utility of bronchoalveolar lavage in immuno-
compromised hosts. Mayo Clin Proc. 1992;67:221–7.
Raab SS, Cheville JC, Bottles K, Cohen MB. Utility of Gomori methen-
amine silver stains in bronchoalveolar lavage specimens. Mod Pathol.
1994;7:599–604.
Saad RS, Silverman JF. Respiratory cytology: differential diagnosis and
pitfalls. Diagn Cytopathol. 2010;38:297–307.
Sheehan MM, Coker R, Coleman DV. Detection of cytomegalovirus
(CMV) in HIV+ patients: comparison of cytomorphology, immunocy-
tochemistry and in situ hybridization. Cytopathology. 1998;9:29–37.
hgbjkdfg
7
Gastrointestinal and
Hepatobiliary Infections
Robert M. Najarian and Helen H. Wang
Department of Pathology, Beth Israel Deaconess Medical Center/Harvard
Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
The diagnosis of gastrointestinal and hepatobiliary infections can

be effectively made by the use of endoscopic brushings, touch
imprints of endoscopic mucosal biopsies, as well as fine needle
aspiration (FNA), or a combination of the above modalities with
concomitant histologic evaluation, microbiologic culture, and
relevant laboratory data (e.g., stool examination). This chapter
discusses characteristic infections of the gastrointestinal and hepa-
tobiliary tracts and focuses on their cytomorphology, differential
diagnosis, and ancillary studies.
Gastrointestinal Infections
Fungal Esophagitis
●● Fungal esophagitis in both immunocompetent and immunocom-
promised patients results mainly from infection by Candida spp.
●● More rare forms of fungal esophagitis in immunocompromised
patients include those caused by dimorphic fungi, Aspergillus
spp., and the zygomycetes.
●● Infection typically presents in the mid to lower esophagus with
symptoms of dysphagia or odynophagia. However, patients can
be asymptomatic, especially those who are immunocompetent.

162 7. Gastrointestinal and Hepatobiliary Infections
●● Predisposing factors include damage to the esophageal mucosal

barrier (chemotherapy, antibiotic use, indwelling devices such as
naso- or orogastric tubes) and a compromise of the host defense
mechanism (such as neutropenia).
●● Sensitivity for diagnosis via brushing closely approximates and,
in some studies, exceeds that of the mucosal biopsy.
●● Infection with Candida spp. manifests with pseudohyphae or
budding yeast forms that stain blue to pink with the Papanico-
laou stain.
●● In contrast, true branching hyphae forming 45° angles in the
setting of a severely debilitated patient confirms the diagnosis
of Aspergillus infection.
●● Predominance of admixed neutrophils with reactive squamous cells
and focal necrosis may be seen in the background (Fig. 7.1).
●● Squamous epithelial reactive changes and an associated neu-
trophilic infiltrate can mimic those seen in viral esophagitis or
ulcers due to direct chemical injuries to the mucosa.
●● Flattened, desquamated anucleate squames, or ingested food can
approximate the appearance of fungal pseudohyphae, but can be
definitively ruled out by lack of staining of these elements with
a PAS plus diastase stain.
●● Oral flora in coccoid forms can be mistaken for yeast forms;
however, no budding will be demonstrated and deployment of
the brushing device in the tubular esophagus below the level of
the oral cavity should eliminate the risk of such bacterial con-
tamination.
●● Filamentous (leptothrix-type) organisms may be associated with
esophageal malignancies. These may resemble actinomyces
clumps.
Ancillary Studies
●● PAS plus diastase or methanamine silver stains will outline
hyphae, pseudohyphae, as well as budding yeast forms.
Gastrointestinal Infections 163
Fig. 7.1. (Left) Brushing preparation of Candida esophagitis with blue-

staining pseudohyphae and purple-staining budding yeast forms (Pap
stain, high magnification). Rare inflammatory cells are seen in the back-
ground. (Right upper) Candida esophagitis is shown in association with
reactive squamous cells (Pap stain, high magnification). (Bottom right)
Superficial esophageal mucosal biopsy showing colonization by Candida
(GMS stain, high magnification).
●● Fungal culture, while not time efficient for diagnosis, can help to
guide antimicrobial therapy and to identify species with resist-
ance to standard antifungal agents.
Herpes Simplex Viruses

●● HSV infection occurs in both immunocompromised and immu-
nocompetent individuals, presenting clinically with acute onset
of odynophagia, fever, and atypical chest pain.
●● In most cases, active infection represents reactivation of latent
infection in immunocompetent individuals.
●● Endoscopically there may be discrete, punched-out ulcers with
an exudative base and erythematous margins. The edge of the
Fig. 7.2. Esophageal brushings demonstrating a multinucleated squamous

cell (left) with nuclear molding as well as nuclear chromatin margination
and (top right) typical Cowdry A inclusions (Pap stain, high magnifica-
tion). (Bottom right) An image from an esophageal mucosal biopsy is
shown demonstrating similar multinucleated squamous cells (arrow) with
nuclear molding and ground glass cytoplasmic change in a background
of necrotic and exudative material characteristic of herpes viral infection
(H&E stain, intermediate magnification).
ulcer should be brushed to identify herpetic changes within

squamous cells and not the ulcer base with granulation tissue.
●● Diffuse and sometimes confluent ulceration is more common in
an immunocompromised patient (Fig. 7.2).
●● Esophageal brushings demonstrate large, glassy, eosinophilic
(Cowdry A) inclusions of the squamous epithelial cell nucleus,
with peripherally condensed margin of chromatin.
●● Multinucleation of squamous cells with molding of the nuclei to
each other and ground glass cytoplasmic change (Cowdry B) are
also characteristically seen.
●● Background neutrophils and necrotic debris may also be present.
●● Reactive cytologic changes seen adjacent to ulcers of varying
etiologies, as well as other infectious conditions, can mimic those
of herpes esophagitis. However, the presence of multinucleated
squamous cells with intracellular inclusions is fairly characteristic.
●● Carcinoma, since viral inclusions may be misinterpreted as
macronucleoli of malignant cells.
●● Radiation esophagitis can produce enlarged squamous cells
with degenerative changes that can simulate ground-glass type
viral inclusions.
●● Cytomegalovirus infection.
Ancillary Studies
●● Immunohistochemical stains for HSV 1 and 2 can increase the
sensitivity for detection of viral cytopathic effect.
●● Viral culture samples, while being highly sensitive for the diag-
nosis of HSV, also have the limitation of requiring days to weeks
for the characteristic cytopathic effect to develop in vitro.
●● Detection of viral DNA by PCR on blood samples is sensitive,
but not specific, for esophageal infection by herpes viruses.
Cytomegalovirus
●● CMV infection of the gastrointestinal tract occurs primarily in
the immunosuppressed patient population, including solid organ
and stem cell transplant recipients, as well as in patients receiv-
ing immunosuppression therapy.
●● Patients may present clinically with nonspecific symptoms such
as epigastric or abdominal pain, nausea, vomiting, and diarrhea.
CMV infection of endothelial cells may also result in ischemic
necrosis with subsequent ulceration and/or pseudotumor forma-
tion causing bowel obstruction.
●● Endoscopy shows punched-out ulcers in the esophagus, stomach,
and/or colon with surrounding erythema (Fig. 7.3).
●● Mucosal brushings and biopsies demonstrate enlargement of
infected endothelial or mesenchymal cells with a characteristic
Fig. 7.3. (Left) Esophageal brushing demonstrating marked enlargement

of esophageal endothelial cells with a prominent eosinophilic nuclear
inclusion and surrounding cleared-out halo (Pap stain, high magnifica-
tion). (Right) A characteristic endothelial cell infected by cytomegalo-
virus is shown (arrow) within the colonic submucosa. The eosinophilic
nuclear inclusion in this case could be mistaken for an enlarged, oval-
shaped nucleolus but was immunoreactive for antibodies to CMV (H&E
single, eosinophilic, intranuclear inclusion, often with a circum-

ferential clear halo surrounding it.
●● Infected cells of mesenchymal origin can also demonstrate
intracytoplasmic, basophilic granules.
●● Focal necrotic debris, scattered neutrophils, fibrinopurulent
exudate, and reactive squamous cells or glandular cells are often
seen in the background.
●● Nucleoli of reactive squamous cells or adenocarcinoma
●● Enlarged endothelial cells within granulation tissue of an ulcer
●● Herpes simplex virus Cowdry A inclusions
●● Immunoblasts or follicular dendritic cells associated with a

reactive lymphoid aggregate or mucosa-associated lymphoid
tissue
Ancillary Studies
●● Immunocytochemical stain for cytomegalovirus can increase
sensitivity for detection of viral cytopathic effect from about 50
to 70% based on H&E evaluation alone to approximately 85%.
●● CMV DNA viral load performed on a blood specimen is
extremely sensitive for detecting infection, but is not predictive
of systemic disease, which requires demonstration of the organism
in a mucosal biopsy or sampling.
Helicobacter pylori Gastritis

●● This bacterial infection is the most common cause of gastritis in
the developing world, with up to 75% of individuals infected by
the age of 25 years, and the most common cause of infectious
gastritis in the developed world.
●● Clinically, patients may present with nonspecific symptoms
such as abdominal or epigastric pain, dyspepsia, and nausea,
while others remain asymptomatic carriers of infection.
●● Gastric infection with Helicobacter pylori has been linked to the
development of the majority of gastric and duodenal ulcers, as
well as to extranodal marginal zone lymphomas of the stomach,
and the intestinal type of gastric adenocarcinoma (Fig. 7.4).
●● Specimens obtained via touch imprints of endoscopic mucosal
biopsies reveal a flagellated, curved, or spiral bacterium (S or
C shaped) measuring 0.3 mm in width and 3–5 mm in length,
often in a background of mucus with superficial gastric foveolar
epithelial cells.
●● The presence of associated lymphoplasmacytic inflammation
(chronic gastritis) with scattered neutrophils (active gastritis) is
variable.
●● Glandular epithelial cells may show reparative atypia and intes-
tinal metaplasia.
●● Candida spp. may also be present if they have colonized an
associated peptic ulcer.
Fig. 7.4. Numerous curved H. pylori organisms are demonstrated in this

imprint obtained from a gastric mucosal biopsy. Note the abundant mucus
layer within which the organisms are seen (Pap stain, high magnification).
●● Infection with other related spiral-shaped bacteria, such as Heli-
cobacter heilmanii can be excluded based upon morphology
alone, in that the latter bacterium is both larger in size (up to
7.5 mm) and more tightly coiled.
●● Debris caught in the superficial gastric mucin layer can often
cause diagnostic difficulty. This can be definitively resolved
with ancillary studies.
●● Contamination of slides with oral flora or environmental bac-
teria, some of which may stain using nonspecific ancillary
methods noted below, are chiefly excluded by the presence of a
polymorphous bacterial population.
Ancillary Studies
●● Special stains that increase the sensitivity of Helicobacter detec-
tion such as the silver-based Steiner, Warthin-Starry, Diff-Quik,
and Giemsa stains will nonspecifically also stain bacterial

contaminants and debris. The bacteria are Gram-negative.
●● Immunocytochemical stains for Helicobacter spp. are sensitive
and specific for organism detection, but stain both H. pylori and
atypical Helicobacter spp.
●● Urease breath tests and the CLO slide test for the urease enzyme
are utilized for detection of infection with fair rates of sensitivity.
●● Serologic tests for H. pylori can aid in documenting a patient’s
history of past infection and guide future ancillary tests per-
formed on mucosal samples.
●● PCR
●● Microbiologic culture
Cryptosporidiosis
●● This gastrointestinal infection, caused by the intracellular pro-
tozoal parasite Cryptosporidium parvum, is most frequently
acquired through the ingestion of contaminated water or by
fecal–oral route.
●● While seen as a rare, self-limited infection in immunocompe-
tent individuals, systemic infection in those who are immu-
nocompromised, especially patients with AIDS, may involve
the entire length of the gastrointestinal tract, including the
gallbladder.
●● Clinically, immunocompetent patients present with a short dura-
tion of diarrheal illness including abdominal cramps and mild
malabsorption. Those with impaired immune function may have
a protracted course with severe weight loss, cholera-like watery
diarrhea, and frequent rates of relapse (Fig. 7.5).
●● Specimens obtained via stool sampling or endoscopic brush-
ings/mucosal biopsies demonstrate spherical organisms meas-
uring 2–5 mm that irregularly protrude from the apical aspect of
the surface epithelium. The microorganisms appear to be adher-
ent to the epithelial cells.
●● Background inflammation is typically not present, but may be
seen in the setting of intense infections.
Fig. 7.5. (Left) Gastric brushing specimen demonstrating many small

spherical organisms adherent to the apical surface of epithelial cells (Pap
stain, high magnification). (Top right) Similar gastric brushing specimen
demonstrating the small spherical organisms (arrow) in a background of
reactive appearing glandular epithelial cells and lack of significant inflam-
mation (Pap stain, high magnification). (Bottom right) Mucosal biopsy
with evidence of Cryptosporidium infection. Note that these small organ-
isms (arrow) are located at the apical surface of the mucosal cells (i.e.,
intracellular but “extracytoplasmic”) (H&E stain, high magnification).
●● Cellular debris and apical mucin adherent to epithelial surfaces
can mimic cryptosporidial infection and sometimes require the
use of ancillary detection techniques.
●● Cyclospora cayetanensis are also located apically within entero-
cytes, but are larger (8–10 mm) and GMS negative.
●● Microsporidiosis, where multiple microorganisms are collec-
tively located within a supranuclear intracytoplasmic vacuole.
●● Isospora belli are located within deeper intracytoplasmic vacuoles,
and are oval and larger (20 mm).
Ancillary Studies
●● Modified acid fast and silver-based stains (such as Steiner or
Warthin-Starry stains) are of benefit in the detection of crypt-
osporidial infection. They are GMS negative.
●● Immunocytochemical stain for Cryptosporidia.
●● Stool examination (modified acid fast stain).
●● Direct and indirect immunofluorescence microscopy can
increase the detection rate of oocysts in stool samples.
●● Transmission electron microscopy.
Giardiasis
●● This is the most commonly diagnosed intestinal parasitic infec-
tion in both the United States and worldwide.
●● Infection caused by the extracellular protozoal parasite Gia-
rdia lamblia (Giardia intestinalis) is most frequently acquired
through the ingestion of contaminated water, typically untreated
water from springs or lakes or via the fecal–oral route in child
care settings.
●● In the acute phase, a self-limited, but severe diarrheal illness can
result in volume depletion while chronic infection can result in a
severe malabsorptive state with iron and folate deficiency.
●● Commonly associated symptoms include abdominal pain, cramp-
ing, nausea, and vomiting with acute illness and weight loss,
malabsorption, and malnutrition in chronic illness (Fig. 7.6).
●● Specimens obtained via stool sampling, endoscopic brushings,
or mucosal biopsy imprints demonstrate flagellated, pear-shaped
organisms similar in size to the nuclei of intestinal epithelial
cells (12–15 mm in greatest dimension).
●● Parasites have a centrally placed nucleus that is gray to
lightly basophilic with the most common cytologic staining
preparations.
●● Extracellular debris can rarely mimic giardial infection.
Fig. 7.6. (Top left) Single, pear-shaped Giardia trophozoite is present in a

duodenal brushing specimen with two prominent, centrally placed nuclei
(Pap stain, high magnification). (Right) Multiple organisms are seen
(arrow) overlying the villous epithelial surface in a duodenal mucosal
biopsy (H&E stain, high magnification). (Bottom left) Immunostaining of
a duodenal mucosal biopsy with antibodies to c-kit demonstrates positive
staining of Giardia organisms (high magnification).
Ancillary Studies
●● Stool examination for ova and parasites, while reasonably sen-
sitive for organism detection in the setting of active infection,
often requires multiple samples to achieve high levels of diag-
nostic sensitivity.
●● Fecal antigen detection and stool PCR tests are available for
sensitive and specific organism detection.
●● An immunostain for c-kit (CD117) can be used to highlight tro-
phozoites and distinguish them from extracellular debris.
Microsporidiosis
●● This is one of the most common gastrointestinal opportunistic
infections in the setting of HIV/AIDS.
Fig. 7.7. (Left and top right) Brushing from the biliary epithelium dem-
onstrates glandular epithelial cells with an intracellular cluster (arrow) of
numerous round spores with a purple color on Papanicolaou stain. Nearby
epithelial cells display a mild increase in nuclear to cytoplasmic ratio and
prominent nucleoli (Pap stain, high magnification). (Bottom right) Micro-
sporidia spores within an intestinal epithelial cell (arrow) are readily visible
with a Brown-Brenn Gram stain (high magnification).
●● Microsporidia include the obligate intracellular parasites Ente-

rocytozoon bieneusi and Encephalitozoon intestinalis.
●● Despite clinical symptoms of watery diarrhea that are mild
relative to other opportunistic organisms, the propensity for
systemic dissemination is great with biliary tract, colonic, respi-
ratory tract and pancreatic infection.
●● Mild infection presents with a normal endoscopic appearance,
while severe cases can have extensive ulcers (Fig. 7.7).
●● Specimens obtained via mucosal biopsy demonstrate intestinal
epithelial cells with oval-shaped, supranuclear spores measuring
approximately 1 mm in diameter.
●● Special care must be taken to examine sampled degenerating

enterocytes for organisms, as there is a greater likelihood of detec-
tion of these microorganisms in the setting of degeneration.
●● Supranuclear mucin vacuoles of oval shape can mimic micro-
sporidia organisms. Problematic cases can be stained with muci-
carmine to demonstrate intracytoplasmic mucin.
Ancillary Studies
●● Acid fast, silver-based, Gram, and PAS stains can all help with
organism detection, as its small size and intracellular location
can easily lead to a false negative diagnosis.
●● Ultrastructural examination is useful in cases in which a particu-
lar species of organism must be isolated or for confirmation of
light microscopic findings.
Mycobacterium avium Complex

●● Extrapulmonary disseminated infection due to atypical myco-
bacteria occurs almost exclusively in the HIV/AIDS population,
especially those with very low CD4 cell counts. Involvement of
the gastrointestinal tract is nearly twice as common as pulmo-
nary involvement.
●● Infection is mainly due to the Mycobacterium avium complex or
MAC (also called Mycobacterium avium intracellulare or MAI).
●● The entire tubular gastrointestinal tract may be involved in such
infections, with the small intestine being the site of most pro-
nounced disease.
●● Clinical symptoms and signs are nonspecific with nausea,
chronic diarrhea, abdominal pain, and malabsorption being
most commonly reported (Fig. 7.8).
●● Specimens obtained via brushings or mucosal biopsies dem-
onstrate organisms with a characteristic “beaded rod” shape
measuring 4–6 mm in length contained either within foamy his-
tiocytes or seen lying free in the background.
Fig. 7.8. Duodenal brushing specimen demonstrating infected macro-

phages with copious foamy cytoplasm (due to negative images of mycobac-
terial organisms within the cytoplasm of macrophages). Note the many free
scattered unstained mycobacteria in the background (Diff-Quik stain, high
magnification). The bottom right inset shows a macrophage stained with an
acid fast stain that demonstrates the mycobacteria (high magnification).
●● The negative (clear or unstained) image of these mycobacteria

may be apparent with a Diff-Quik stain.
●● Rarely, poorly formed granulomas comprised of aggregates of
organism-laden histiocytes can be observed, but much less fre-
quently than in cases of Mycobacterium tuberculosis infection.
●● Whipple’s disease and histoplasmosis are diagnostic considera-
tions, which are both Periodic acid Schiff stain positive, but acid
fast negative.
Ancillary Studies
●● Acid fast stain of cytologic preparations or formalin fixed tissue
biopsy.
●● PCR analysis.
●● Mycobacterial culture is both sensitive and specific for organ-
ism detection, but requires weeks to months to achieve adequate
organism growth.
Anal Pap Test

●● The incidence of anal intraepithelial neoplasia (AIN) and inva-
sive anal cancer is increasing, especially in the HIV population.
●● Anal Pap tests have been utilized in the HIV population for the
evaluation of HPV-related disease of the anus. The sensitivity
(42–98%) and specificity (16–96%) of the anal Pap test for the
detection of squamous intraepithelial lesions (SIL) are quite variable.
●● It is recommended that anal–rectal cytologic findings be reported
according to the criteria and terminology of the Bethesda System
(2001) used for reporting cervical cytology.
●● Cellular elements that may be encountered in an anal Pap test
include:
Squamous cells, anucleate squames, and anal transformation
zone components (metaplastic cells and/or rectal glandular

cells).
HPV-related diseases include SIL and squamous cell carci-
noma. SIL tend to, but not always, exhibit prominent kerati-
nization.
Contamination with bacteria and fecal material, which may
obscure cells, making the specimen unsatisfactory for evalu-

ation.
Less commonly, infectious organisms other than HPV can
be detected such as Candida spp., herpes simplex virus,

trichomonas, and other parasites including ova and worms
(Fig. 7.9).
Intra-Abdominal Infections
Liver Abscess
●● The majority of liver abscesses are due to bacterial infections.
Pyogenic abscesses are mainly due to streptococci, staphylococci,
or enteric bacteria. They may occur as a result of ascending
Intra-Abdominal Infections 177
Fig. 7.9. Anal Pap test showing an incidental finding (arrow) of a patho-
genic ameba (higher magnification shown in the upper left inset) con-
taining phagocytosed erythrocytes (Pap stain, high magnification) (image
courtesy of Christine Panetti CT (ASCP), Baystate Medical Center,
Springfield, MA, USA).
cholangitis, sepsis, or following trauma. Not all patients have

a fever or right upper quadrant tenderness. FNA contains abun-
dant neutrophils with necrotic debris and occasionally bacteria
that can be readily confirmed with a Gram stain.
●● Candida is the most common cause of an hepatic fungal abscess,
and usually encountered in patients with an impaired immunity.
Other organisms that may be encountered in an FNA of a liver
abscess include actinomyces, Leishmania, and G. lamblia.
●● Hepatic amebic abscess, due mainly to infection with Entameba

histolytica, is an uncommon complication of amebiasis involv-
ing the gastrointestinal tract. They mainly involve the right liver
lobe. FNA material contains trophozites associated with abun-
dant necrotic debris (“anchovy paste”), macrophages, degener-
ated hepatocytes, and only scant neutrophils. Trophozoites of
E. histolytica resemble macrophages with their round shape,
foamy cytoplasm, and single round nucleus. They typically con-
tain phagocytosed red blood cells.
●● The finding of numerous eosinophils may be related to parasites,
such as the liver flukes Clonorchis sinensis or Fasciola hepatica.
●● FNA material containing granulomas may be seen and due to
infection (e.g., tuberculosis, fungi) or other liver disorder (e.g.,
primary biliary cirrhosis, sarcoidosis, drug reaction, etc.).
●● The differential diagnosis of a liver abscess includes a neoplasm
with marked tumor necrosis (Fig. 7.10).
Pancreatitis
●● Pancreatitis (usually acute) may be caused by a variety of infec-
tions including viruses (e.g., mumps, HSV, HIV), bacteria (e.g.,
mycoplasma, salmonella), fungi (e.g., Aspergillus), and parasites
(e.g., Toxoplasma, cryptosporidium, Ascaris). FNA is typically
not performed in patients with acute pancreatitis, but if performed
will show numerous neutrophils with fat necrosis, epithelial cells
with inflammatory atypia, and a dirty background.
●● Microorganisms may be detected in cytology material or can be
cultured from aspirated material submitted to the microbiology
laboratory.
●● As pancreatitis may occur secondary to obstruction from a
neoplasm, a careful search for associated neoplastic cells is
important.
Hydatid Disease
●● Echinococcosis (hydatid disease) is caused by ingestion of
the larval forms of Echinococcus tapeworms, most commonly
Echinococcus granulosus, which spread via the portal venous
circulation to the liver.
Fig. 7.10. (Left) Liver abscess following cholecystectomy in this case

was found to be due to actinomyces on FNA. A sulfur granule is shown
containing filamentous bacteria surrounded by many neutrophils (Gram
stain, high magnification). (Right) Percutaneous liver FNA of an amebic
liver abscess shows an ameba present (arrow) in an inflamed background
(Pap stain, high magnification) (image courtesy of Dr. Pam Michelow,
South Africa).
●● Patients commonly present with a slowly growing hydatid cyst

identified either incidentally on an imaging study or after epi-
sodes of abdominal pain, jaundice, or portal hypertension in
cases of larger cysts.
●● The diagnosis is often made preliminarily on abdominal imag-
ing studies following the identification of a thin-walled cyst in
the setting of positive serologic studies (Fig. 7.11).
●● A confirmatory diagnosis can be made by FNA of hepatic cystic
lesions that demonstrate ovoid protoscoleces measuring about
100 mm in diameter that are attached to the germinal membrane
of the cyst wall.
Fig. 7.11. Fine needle aspirate of hydatid cyst fluid demonstrates a pro-
toscolex with radial array of hooklets with a (left) Papanicolaou stain and
(top right) Diff-Quik stain (high magnification). (Lower right) Hydatid
cyst fluid is shown to contain only scattered hooklets without an associ-
ated protoscolex. Note their characteristic scimitar shape (Diff-Quik stain,
high magnification) (image courtesy of Thomas Buck, M.D., Beth Israel
Deaconess Medical Center, Boston, MA).
●● Intact protoscoleces contain two circular arrays of hooklets and

a sucker. However, cysts often contain only shed hooklets or
degenerated material (hydatid sand).
●● Shed hooklets are said to have a characteristic scimitar (curved,
single-edged sword) shape that may be accompanied by calcare-
ous bodies.
●● Differentiation of a viable hydatid cyst from simple benign
hepatic cysts or mesothelial inclusion cysts rests on the ability
to demonstrate any viable components of the hydatid cyst
including the protoscoleces, hooklets, or germinal membrane.
Surgical excision with extensive sampling of tissue for histopa-

thology is often required to demonstrate these components.
Ancillary Studies
●● Serologic studies for antibodies to E. granulosus
Peritoneal Effusion with Infection

●● Intraperitoneal infection may be diffuse (peritonitis), localized
(intraperitoneal abscess), or abscess may form around diseased
viscera (e.g., periappendiceal abscess).
●● Secondary intra-abdominal infection may result from spillage of
gastrointestinal or genitourinary microorganisms into the perito-
neal cavity (e.g., trauma, abdominal surgery, perforated appendici-
tis, or diverticulitis). These infections are typically polymicrobial.
●● Primary peritonitis (also called spontaneous bacterial peritoni-
tis) occurs in patients of all ages and may be associated with
ascites, cirrhosis, or nephrotic syndrome.
Microorganisms that cause primary peritonitis include bacteria
of enteric origin (e.g., Escherichia coli, Klebsiella) and strep-

tococci. Culture negative cases have also been described.
Peritoneal fluid or ascites contain many neutrophils
(>250 cells/mm3 is diagnostic of primary peritonitis irrespec-
tive of the culture results). A Gram stain along with cultures
is also diagnostic.
●● Effusions with fungal infections are usually the result of dis-
seminated infection in an immunocompromised host. Fungi that
may be identified include Candida spp., Aspergillus, Crypto-
coccus, and several of the dimorphic fungi.
●● Infection is usually associated with a significant inflammatory
background. Depending on the host, evolution of the infection
and treatment there may be mainly acute or chronic inflamma-
tory cells present.
●● Parasitic infections are often accompanied by many eosinophils.
Other causes of increased eosinophils in peritoneal fluid include
peritoneal dialysis, allergy, eosinophilic gastroenteritis, collagen
vascular disease, and neoplasia (leukemia/lymphoma) including
hypereosinophilic syndrome.
Suggested Reading
Bean SM, Chhieng DC. Anal-rectal cytology: a review. Diagn Cytopathol.
2010;38:538–46.
Huppmann AR, Orenstein JM. Opportunistic disorders of the gastrointes-
tinal tract in the age of highly active antiretroviral therapy. Hum Pathol.
2010;41:1777–87.
Kotler DP, Giang TT, Garro ML, Orenstein JM. Light microscopic diag-
nosis of microsporidiosis in patients with AIDS. Am J Gastroenterol.
1994;89:540–4.
Marshall JB, Kelley DH, Vogele KA. Giardiasis: diagnosis by endoscopic
brush biopsy of the duodenum. Am J Gastroenterol. 1984;79:517–9.
Muir SW, Murray J, Farquharson MA, Wheatley DJ, MCPhaden AR.
Detection of cytomegalovirus in upper gastrointestinal biopsies from
heart transplant recipients: comparison of light microscopy, immuno-
cytochemistry, in situ hybridization, and nested PCR. J Clin Pathol.
1998;51:807–11.
Ramanathan J, Rammouni M, Baran J, Khatib R. Herpes simplex esophag-
itis in the immunocompetent host: an overview. Am J Gastroenterol.
2000;95:2171–6.
Senturk O, Canturk Z, Ercin C, et al. Comparison of five detection methods
for Helicobacter pylori. Acta Cytol. 2000;44:1010–4.
8
Urinary Tract Infections
Walid E. Khalbuss, Liron Pantanowitz,
and Anil V. Parwani
Infections of the urinary tract can be classified into upper

(pyelonephritis) and lower tract infections (ureteritis, urethritis,
and cystitis). This chapter also covers male genitourinary infec-
tions. Urologic specimens submitted for cytologic examination
mainly include urine cytology, but specimen procurement may
involve FNA. Apart from detecting infections (viral, bacterial,
fungal, or parasitic), cytology can diagnose malignancy masquer-
ading as an infection. Transplant related infections of the kidney
are covered in Chap. 13.
Kidney Infections
In general, the morphologic characteristics of infectious agents
that affect the kidney are similar to those present in other organs.
Acute Pyelonephritis
●● Acute infection of the renal parenchyma and pelvis usually
results from a bacterial infection of the kidney, most commonly
with Escherichia coli ascent via the urethra. Other etiological
agents include Staphylococcus and Enterococci. Hematogenous
spread of microorganisms to the kidney can cause a renal abscess
that presents as a kidney mass.

184 8. Urinary Tract Infections
●● Infections in diabetic patients may be due to Klebsiella, Entero-

bacter, Clostridium, Candida and are rarely of viral etiology.
●● Risk factors include abnormal kidneys (e.g., polycystic or horse-
shoe kidney), vesicoureteric reflux, foreign body, instrumenta-
tion, and immunosuppression.
●● Infected kidneys are infiltrated with neutrophils and may result
in abscess formation, ischemic necrosis, and cystic change.
●● White blood cell (WBC) casts in urine samples are characteristic
of acute bacterial pyelonephritis, but are not always seen.
●● FNA of a renal or perirenal abscess contains mainly neutrophils
as well as chronic inflammatory cells and necrosis.
●● Viral inclusions (cytomegalovirus [CMV], polyoma (BK) virus,
adenovirus) may be seen in renal tubular cells.
●● Fungal casts may be identified. However, filamentous fungi may
not be present in voided urine specimens, and their diagnosis
may require direct ureteral or renal pelvis catheterization.
●● Overgrowth of bacteria or yeast (no inflammation is present).
Ancillary Studies
●● Urinalysis: >5 WBCs/HPF
●● Positive leukocyte esterase and nitrite tests
●● Gram stain for bacterial infection
●● GMS stain for fungal infection
●● Urine microbiology culture
Chronic Pyelonephritis
●● Chronic pyelonephritis is the result of a persistent renal infection
that may lead to chronic renal failure and small scarred kidneys.
●● Such chronic infections occur in patients with major anatomical
anomalies, renal stones, obstructive uropathy, or vesicoureteral
reflux. Obstruction leads to urine stasis which in turn results in
infection.
Kidney Infections 185
●● The urine cytology of chronic pyelonephritis is nonspecific and
may include variable numbers of inflammatory cells, a granular
background (amorphous debris) indicative of tissue damage,
and casts (broad waxy, hyaline, and granular casts).
Differential Diagnosis and Ancillary Studies

●● Same as acute pyelonephritis
Xanthogranulomatous Pyelonephritis (XPN)

●● Xanthogranulomatous pyelonephritis (XPN) is a chronic
destructive granulomatous inflammatory process of the kidney
associated with obstruction due to infected renal stones.
●● Positive urine cultures frequently show E. coli and Proteus
mirabilis, and less often Pseudomonas, Streptococcus faecalis,
and Klebsiella. In approximately 25% of cases urine cultures
may be sterile.
●● Patients are typically middle-aged women with a history of
recurrent urinary tract infections. They may present with flank
pain, fever, hematuria, pyuria, calculi, and a unilateral mass
that mimics cancer. Imaging of the kidney often shows multiple
nodules, calculi (often staghorn type), and perirenal extension.
●● The histopathology is characterized by a focal or diffuse
granulomatous mixed inflammatory infiltrate (neutrophils,
lymphocytes, plasma cells, and multinucleated giant cells)
associated with xanthomatous histiocytes (foamy cytoplasm),
spindle cell proliferation, microabscesses, fibrosis, renal
tubular atrophy, and squamous metaplasia of the urothelium
(Fig. 8.1).
●● FNA specimens contain vacuolated histiocytes admixed with
acute and chronic inflammatory cells, as well as occasional
multinucleated giant cells.
●● The findings in urine are nonspecific and may show an intense
inflammatory and/or hemorrhagic background.
Fig. 8.1. Xanthogranulomatous pyelonephritis (XPN). The images shown

are from an FNA of XPN presenting as a renal mass in a 70-year old
female. The specimen is cellular and shows numerous clusters of inflam-
matory cells (left image, Pap stain, low magnification) that consist largely
of histiocytes with vacuolated cytoplasm (foam cells) present in a back-
ground of granular debris, neutrophils, and lymphocytes (middle and right
images, Pap stain, high magnification).
●● Squamous metaplastic cells may be numerous in FNA and urine

samples.
●● A predominant spindle cell component may be mistaken for
sarcomatous renal cell carcinoma. Fat necrosis may mimic
lipoblasts.
●● Bacteria are usually not identified, although basophilic intracy-
toplasmic PAS-negative inclusions have been reported.
●● Nonspecific inflammatory response (requires clinical and radio-
logic correlation)
●● Inflammatory diseases with giant cells such as tuberculosis
Kidney Infections 187
●● Other entities with foamy histiocytes such as malakoplakia.

(XPN does not contain Michaelis-Gutmann bodies).
●● Clear cell renal cell carcinoma involving the renal pelvis may
exfoliate malignant cells in urine. Unlike foamy histiocytes of
XPN, carcinoma cells have cytological atypia, higher N:C ratio,
mitoses, and a prominent nucleolus. The stroma in XPN resem-
bles granulation tissue, whereas the vascular network in renal
cell carcinoma tends to be more delicate. XPN may be associ-
ated with urologic tumors in up to 4% of cases.
Ancillary Studies
●● Gram stain for associated bacteria.
●● Immunostains to characterize macrophages (cytokeratin and
EMA negative, S100 and CD68 positive) in difficult cases.
Renal Tuberculosis
●● Mycobacterium tuberculosis seeding of the kidney usually
follows hematogenous spread from another infected site (e.g.,
pulmonary TB).
●● Atypical mycobacteria may also cause renal disease (e.g., Myco-
bacterium avium-intracellulare and M. bovis).
●● Infection is characterized by caseating granulomatous inflam-
mation, chronic interstitial inflammation, thyroidization of
tubules, glomerulosclerosis, fibrosis, calcification, and stricture
formation resulting in obstruction.
●● Urine specimens usually show sterile pyuria.
●● FNA material contains epithelioid granulomas, multinucleated
Langhans-type giant cells, and a granular necrotic background.
●● Other necrotizing granulomatous infections (e.g., fungal infection).
●● Benign non-necrotizing granulomatous conditions (e.g., sar-
coidosis).
●● Granulomas associated with malignancy (e.g., lymphoma,
seminoma).
●● XPN
●● Malakoplakia
●● Malignancy that mimics granulomas (e.g., renal cell carcinoma)
Ancillary Studies
●● Special stains for acid-fast mycobacteria
●● PCR to confirm the diagnosis and identify species
●● Microbiology cultures
Fungal Kidney Infections

●● Common fungal infections of the kidney include Candida
(C. albicans and C. glabrata), Aspergillus, Cryptococcus, Coc-
cidioides, Histoplasma, Blastomyces, and Mucor spp.
●● Infection typically arises from hematogenous spread. Candida
may originate from the gastrointestinal tract, particularly in
patients with nephrostomy tubes.
●● Patients at increased risk of fungal infection are immunosup-
pressed individuals.
●● Fungi may evoke a granulomatous inflammatory reaction with
or without necrosis, cause abscesses, and even manifest with
renal infarcts.
●● Urine usually shows nonspecific findings (e.g., neutrophils, reac-
tive urothelial cells, RBCs). Necrotizing granulomatous inflam-
mation is more likely to be observed in renal pelvic washings.
●● FNA of a fungal mass will show necrotizing granulomatous
inflammation.
●● Fungi including fungal casts may be seen. Depending on the
type of fungal infection specimens may include budding yeast
(e.g., narrow-based budding of Cryptococcus vs. broad-based
budding yeast diagnostic of balstomycosis), pseudohyphae
(Candida spp.), or true hyphae. Fungal organisms may be intra-
cellular within macrophages.
●● Overgrowth of fungi in urine (inflammation is usually absent)
●● Fungal mimics (e.g., contaminants)
Urinary Bladder Infections 189
Ancillary Studies
●● GMS or PAS stains for fungal elements
●● Mucicarmine stain for Cryptococcus
●● Calcofluor stain
●● Microbiology culture
Urinary Bladder Infections

Bacterial Cystitis
●● Bacterial cystitis is commonly caused by Gram-negative bacte-
ria (E. coli, Klebsiella, Enterobacter, Serratia, Pseudomonas,
P. mirabilis) and is infrequently due to Gram-positive bacteria
(Staphylococcus aureus, Staphylococcus saprophyticus, and
Enterococci).
●● Infection occurs from ascending bacterial infection via the distal
urethra, and mostly affects women of reproductive age. Patients
with structural bladder abnormalities and systemic disease such
as diabetes are more susceptible to infection.
●● Symptoms include increased frequency, urgency, dysuria, hema-
turia, and suprapubic pain.
●● Infection typically presents with prominent acute inflammation
in the urine, and sometimes with chronic inflammatory cells in
more long-standing infections.
●● Bacterial colonies may be present. Bacterial morphology is
often altered (e.g., filamentous appearance) following antibiotic
therapy (Figs. 8.2–8.3).
●● Apart from acute inflammatory cells, urine specimens also
demonstrate nonspecific findings (reactive and degenerated
urothelial cells, RBCs, and cellular debris). In chronic infections
there are many more lymphocytes present (Fig. 8.4).
●● Bacterial cystitis may be superimposed on malignancy. There-
fore, admixed atypical or neoplastic urothelial cells should not
be overlooked.
Fig. 8.2. Acute bacterial cystitis. The urine specimen shows a predomi-
nance of neutrophils with bacteria and occasional red blood cells. There
were very few urothelial cells present in this case (left and upper right
images: Pap stain, ThinPrep, high magnification; bottom right image:
H&E stain, cell block, high magnification).
●● Bacterial overgrowth (no inflammatory reaction is present)
●● Bacterial contamination from a neobladder urine specimen
●● Pyelonephritis (which often has associated WBC casts)
Ancillary Studies
●● Gram stain for bacteria
Malakoplakia
●● This is a rare chronic granulomatous disease that primarily
affects the urinary tract, particularly the bladder and ureters.
●● Urine culture often isolates E. coli.
Fig. 8.3. (Top left image) Bacteria in urine exposed to excreted antibiotics
may assume unusual forms, such as these elongated Pseudomonas bacte-
ria identified in this treated patient (Pap stain, high magnification). Vari-
able numbers of bacteria in urine may be encountered (bottom left image)
due to fecal contamination or (right image) in degenerated ileal conduit
samples without associated acute inflammation (Pap stain, intermediate
magnification).
●● The condition is characterized histologically by aggregates of

large histiocytes (von Hansemann cells) containing round cyto-
plasmic and extracellular laminated Michaelis-Gutmann bodies,
thought to contain mineralized bacterial fragments.
●● The cytomorphology in FNA or urine samples shows many
large, foamy, granular macrophages with large, eccentric nuclei,
and prominent nucleoli. Cells containing Michaelis-Gutmann
bodies may be identified, which can be highlighted with the use
of a PAS stain (Fig. 8.5).
Viral Infections
●● Viruses are a rare cause of cystitis, but may be seen in immu-
nosuppressed patients. Immunocytochemistry can be used for
confirmation.
Fig. 8.4. Follicular cystitis. This voided urine specimen shows a pre-
dominance of lymphocytes associated with bacteria (left image; Pap stain,
intermediate magnification; upper right image; high magnification, Pap
stain; lower right image, H&E stain on cell block).
●● Human papillomavirus (HPV) effect of squamous cells (e.g.,

koilocytosis) in urine may be due to contamination from genital
infection or from bladder and/or urethral condylomas. Bladder
condyloma is more common in women than men. Cytological
features are basically the same as those seen in cervicovaginal
Pap tests (Fig. 8.6). HPV has been reported to occur in the blad-
der, and may play a role in urethral carcinoma.
●● Herpes simplex virus (HSV) causes hemorrhagic cystitis, partic-
ularly in patients with genital herpes. Infected cells are enlarged,
multinucleated, exhibit nuclear molding, and margination of
chromatin. Cells with ground glass nuclei and Cowdry A nuclear
inclusions may also be present. Background acute inflammation
is often present.
●● Adenovirus causes hemorrhagic cystitis, especially in children.
Infected cells have large, homogeneous basophilic intranuclear
inclusion bodies.
Fig. 8.5. Malakoplakia of the bladder with large histiocytes containing

cytoplasmic lamellated structures of Michaelis-Gutmann bodies shown in
urine (Pap stain, high magnification). The resection specimen showed that
malakoplakia involved almost the entire bladder with a markedly thick-
ened mucosa (gross pathology, right inset). Michaelis-Guttman bodies
are highlighted by a PAS stain on histological section (right image, H&E
●● CMV can cause hemorrhagic cystitis in immunosuppressed

patients. Infected cells may have intracytoplasmic and nuclear
inclusions, but multinucleation is rare.
BK Polyomavirus
Microbiology
●● BK virus is a member of the polyomavirus family.
●● Infection is usually acquired at an early age. Up to 80% of the
population are likely to have had prior infection.
●● Polyomavirus remains latent within urothelium and kidney
tubular epithelial cells. Changes in host immune status can lead
Fig. 8.6. HPV-related koilocytes are shown in this voided urine specimen
from a 31-year old male. He had a history of known anal condylomas (Pap
to viral reactivation, causing viral particles and infected cells

(so-called “decoy cells”) to be shed into the urine.
●● As decoy cells contain BK virus antigens, in renal allograft recipi-
ents the examination of urine cytology specimens for cells with
polyomavirus inclusions is often used to assess for viral reactiva-
tion, and hence the risk for BK nephropathy. The sensitivity (99%)
and specificity (95%) of decoy cells for diagnosing BK nephropa-
thy is high. While the positive predictive value varies (27–90%),
the negative predictive value is high (99%) (Figs. 8.7 and 8.8).
Clinical Features
●● BK virus in immunocompetent individuals rarely causes disease.
Those people who are infected with this virus are usually asymp-
tomatic, or may manifest with a transient hematuria.
●● Infection in immunocompromised individuals may cause hem-
orrhagic cystitis, ureteral stenosis, and/or progressive renal dys-
function (nephritis).
Fig. 8.7. Decoy cells are shown with viral changes in the (top left) inclu-
sion and (top right) postinclusion stages of BK polyomavirus infection
(Pap stain, high magnification). (Bottom left) A comet cell is shown with
an eccentrically placed glassy appearing nucleus (Pap stain, high magni-
fication). Cells infected with polyomavirus are shown to exhibit nuclear
immunoreactivity with a BK virus immunocytochemical stain (high
magnification).
●● Approximately 1–10% of infected renal transplant patients

progress to BK virus nephropathy, causing many (up to 80%) of
these patients to lose their renal grafts. This may occur within a
few days posttransplant to 5 years later.
●● Other infected patients that may shed slightly increased numbers
of decoy cells include the elderly, pregnant women, and those
with cancer or diabetes mellitus.
●● The detection of decoy cells is easily identified (and even quantifi-
able) in routine Papanicolaou stained urine cytology specimens.
Fig. 8.8. Polyoma virus infection in voided urine from a renal trans-
plant patient. Two types of inclusions in decoy cells can be appreciated
including cells with large homogenous, basophilic, glassy intranuclear
inclusions and those with vesicular nuclei containing clearing of their
chromatin. Note that these cells have no nuclear contour irregularity, an
important distinction from cells of high-grade urothelial carcinoma (Pap
●● There are two types of infected epithelial cells:

Cells with large homogenous (ground-glass like) basophilic
intranuclear inclusions, a condensed rim of chromatin, and
that show some degree of degenerative changes (early stage
of infection).
Cells with vesicular nuclei that have so-called “fish-net stocking”
clearing of their chromatin (late or “empty” stage of infection).

●● Many decoy cells may have eccentric cytoplasm resembling the
tail of a comet (termed “comet cells”).
●● Decoy cells typically are present as single cells, and clustering
of these cells is a rare finding.
●● Occasionally, multinucleated decoy cells may be detected.
●● Decoy cells do not show nuclear contour irregularity and there

is no necrosis, as may be encountered with carcinoma in situ or
high-grade urothelial carcinoma.
●● Polyomavirus infection can coexist with high-grade urothelial
carcinoma.
●● Cytomorphologic changes in urine may persist for several
months after cessation of symptoms.
●● High-grade urothelial carcinoma
●● Degenerated (urothelial) cells. To avoid high levels of cellular
degeneration, it is best to avoid examining the first morning
urine specimen and promptly fix or transport urine to the cytol-
ogy laboratory for immediate processing
●● Radiation or chemotherapy effect
●● Other viral cytopathic change (e.g., adenovirus, herpes, CMV)
Ancillary Studies
●● Immunocytochemistry with Simian virus 40 (SV40) antibody
for BK virus
●● Serology is unhelpful as many people will demonstrate past
infection
●● PCR (quantitative analysis is possible measuring BK virus DNA
loads in serum samples)
●● Electron microscopy
●● Kidney tissue biopsy (gold standard test)
Fungal Infections
Microbiology
●● Bladder fungal infections are mostly caused by C. albicans.
●● Infection may also be due to invasive fungi such as Aspergillus, Blas-
tomyces, Mucor, Histoplasma, Cryptococcus, and Coccidioides.
●● Candidal and bacterial infections frequently occur simulta-
neously.
Clinical Features
●● Fungal infection of the bladder mostly affects women. Risk factors
include immunosuppression, indwelling devices, obstruction,
diabetes, or antibiotic therapy.
●● Most patients with candiduria are asymptomatic. Patients may
also present with urinary symptoms (nocturia, suprapubic pain,
frequency, and hematuria), complications (emphysematous cys-
titis, pyelonephritis, bezoars, abscess, rarely renal failure), and/
or disseminated disease.
●● Infections may cause cystitis with ulceration.
●● Fungal elements are identified in urine. Candida is the most
common fungus seen in urine specimens, and it is also the most
common contaminant.
●● True fungal cystitis should be only suggested if there is associated
acute inflammation and reactive cellular changes. Final diagno-
sis requires clinical and microbiology correlation (Fig. 8.9).
●● Budding yeast and pseudohyphal forms are characteristic of Can-
dida spp., larger yeasts with narrow-based budding surrounded
by clear capsule are characteristic of Cryptococcus, broad-based
budding yeast is diagnostic of blastomycosis, and intracellular
microorganisms are characteristic of histoplasmosis.
●● Nonspecific changes like hematuria may be present.
●● Fungal cystitis may be superimposed on malignancy. Therefore,
a careful search should be carried out for atypical or neoplastic
urothelial cells.
●● Fungal contaminants (usually have no inflammatory reaction)
●● Fungal infection of the kidney (casts are typically present)
●● Fungal mimics
Ancillary Studies
Parasites 199
Fig. 8.9. Acute candida cystitis. This voided urine specimen shows many
acute inflammatory cells and fungal microorganisms. The fungal organ-
isms include budding yeasts and pseudohyphal forms characteristic of
Candida spp. (left and upper right images: Pap stain, high magnification;
bottom right image: H&E cell block, high magnification). The specimen
contains atypical urothelial cells attributed to reactive changes associated
with this fungal infection (left upper inset: Pap stain, high magnification).
●● GMS or PAS stain for identification of fungal forms

●● Mucicarmine stain for Cryptococcus
Parasites
Schistosomiasis
Microbiology
●● Schistosomiasis (also known as bilharzia) is caused by trema-
todes (flukes) of the genus Schistosoma. Schistosoma hemato-
bium causes urinary schistosomiasis.
Fig. 8.10. Bladder schistosomiasis. The images show the ova of Schisto-
soma hematobium recognized by their terminal spine (DQ left, Pap stain
right, high magnification).
●● Worms residing in the urinary bladder venous plexus excrete

eggs in the urine. Eggs that embed in tissue may calcify and
cause urothelial squamous metaplasia, intestinal metaplasia,
granulomas, and eosinophilia.
●● Eggs can also be found in the urine with infections from S. japon-
icum and S. intercalatum. S. mansoni eggs are more common in
stools and rarely seen in urine (Fig. 8.10).
Clinical Features
●● Patients develop chronic cystitis and may present with hematuria.
●● Chronic infection can lead to fibrosis, urinary obstruction, and
rarely urothelial squamous cell carcinoma.
●● Microscopic identification of eggs in urine is the most practical
method for diagnosis of urinary schistosomiasis.
Parasites 201
●● S. hematobium eggs are elliptical and recognized by a terminal

spine, whereas S. japonicum eggs are spheroidal with a small
knob. S. mansoni eggs are identified by their characteristic
lateral spines.
●● Adult worms may be recognized, but are rare. They are small
(12–26 mm long and 0.3–0.6 mm wide) and their size varies
with the different species.
●● Urine specimens may show squamous and intestinal metaplasia,
granulomas, and/or eosinophilia.
●● Squamous cell carcinoma may be present in rare cases.
●● Other parasitic ova
●● Mimics of parasite eggs
Ancillary Studies
●● Microbiology consultation
●● Serum antibody detection
●● Tissue biopsy
Trichomoniasis
●● Trichomoniasis is a sexually transmitted infection caused by the
protozoan Trichomonas vaginalis.
●● Parasites may cause urethritis and cystitis in both women and
men, particularly if there is a coexisting genital infection.
●● The cytomorphology of trichomonads in urine cytology is the
same as in Pap test (refer to Chap. 5). However, when in urine,
trichomonads may assume variable shapes (smaller and more
round in shape).
●● Trichomonas infection can cause an inflammatory reaction,
with a large number of neutrophils usually present in urine
specimens.
●● Immunocytochemistry with p16 (clone G175-405, BD Bio-
sciences Pharmingen, San Diego, CA, USA) and microbiology
culture can help establish the diagnosis of trichomonas in urine
(Fig. 8.11).
Fig. 8.11. Urine trichomoniasis. (Left image) A group of trichomonads,

round in shape and slightly variable in size, is shown in a urine speci-
men from an 80-year-old man (Thin Prep, Pap stain, high magnification).
(Right image) These parasites were p16 positive (immunocytochemical
stain, high magnification) (reprinted from Pantanowitz et al. Diagnostic
utility of p16 immunocytochemistry for Trichomonas in urine cytology.
Cytojournal. 2005;2:11, with permission from Biomed Central Ltd.).
Male Genital Tract Infections

●● Infections of the penis may be localized (e.g., condyloma accu-
minatum) or widespread (e.g., Fournier gangrene). Cytologic
diagnoses of these infections may be obtained by Tzanck prepa-
ration of ulcers, characteristic cells or organisms contaminating
urine samples, or FNA of lesions.
●● Epididymitis is the most common source of intrascrotal infection,
and may extend to involve the testis. Infection of the testes may
be due to viruses (e.g., mumps), bacteria (including syphilis),
malakoplakia, mycobacteria (TB orchitis and leprosy), or fungi
(Candida, Blastomyces, Aspergillus, Histoplasma capsulatum,
Trichophyton mentagrophytes, and Coccidioides immitis).
Male Genital Tract Infections 203
●● In general, acute bacterial infections show suppurative inflam-

mation, whereas the cytomorphology of viral, mycobacterial,
and fungal infections as well as malakoplakia is similar to that
seen in other sites.
Urethritis
●● Urethral infections are typically sexually transmitted and may
be classified as gonococcal uretheritis (GU) or nongonococcal
uretheritis (NGU).
●● GU is caused by the Gram-negative intracellular diplococcus
Neisseria gonorrheae. NGU is due to infection with Chlamydia
trachomatis, Ureaplasma urealyticum, Mycoplasma hominis,
Mycoplasma genitalium, or T. vaginalis.
●● The cytomorphological features in urine include acute and/or
chronic inflammatory cells. NGU typically does not present
with a purulent discharge as with gonorrhea. Intracellular diplo-
cocci may rarely be detected with a Gram stain.
Suggested Reading
Cimbaluk D, Pitelka L, Kluskens L, Gattuso P. Update on human polyo-
mavirus BK nephropathy. Diagn Cytopathol. 2009;37:773–9.
Gupta M, Venkatesh SK, Kumar A, Pandey R. Fine-needle aspira-
tion cytology of bilateral renal malakoplakia. Diagn Cytopathol.
2004;31:116–7.
Kumar N, Jain S. Aspiration cytology of focal xanthogranulomatous pyelone-
phritis: a diagnostic challenge. Diagn Cytopathol. 2004;30:111–4.
Pantanowitz L, Cao QJ, Goulart RA, Otis CN. Diagnostic utility of p16
immunocytochemistry for Trichomonas in urine cytology. Cytojournal.
2005;2:11.
Waugh MS, Perfect JR, Dash RC. Schistosoma haematobium in urine:
morphology with ThinPrep method. Diagn Cytopathol. 2007;35:649–50.
hgbjkdfg
9
Central Nervous System
Infections
Walid E. Khalbuss1, Pam Michelow2,
Sara E. Monaco1, and Liron Pantanowitz1
1
2
Cytology Unit, Department of Anatomical Pathology, University of the
Witwatersrand and National Health Laboratory Service, Corner Hospital Hill
and De Korte Streets, Braamfontein, Johannesburg, Gauteng 2000, South Africa
Infections of the central nervous system (CNS) may involve the

meninges (meningitis), brain matter (encephalitis), or both (menin-
goencephalitis). Additionally, infections can be acute or chronic.
Cerebrospinal fluid (CSF) analysis can be used to diagnose a wide
variety of neoplastic and non-neoplastic conditions including
infectious diseases affecting the CNS. Brain infections can also be
diagnosed by cytology using touch or squash preparations of brain
tissue, often performed at the time of an intraoperative consulta-
tion. Microorganisms that cause CNS infection may be bacterial
(Table 9.1), fungal, parasitic, or viral. Furthermore, prions repre-
sent an unusual class of infectious agent that can damage the brain,
but usually these are not diagnosed using cytology.
A slight increase in the number of leukocytes and macrophages
in CSF is always pathological and should suggest that an infec-
tious or inflammatory process may be present. Polymorphonuclear
leukocytes normally do not cross the blood–brain barrier. Hence,
their presence in CSF is considered pathological. Pleocytosis refers
to an increased number of cells in the CSF (Table 9.2). The type
of pleocytosis is usually based on the dominant cell population.

206 9. Central Nervous System Infections
Table 9.1. Common bacterial infections of the

central nervous system (CNS).
Neonatal meningitis
• Group B beta-hemolytic Streptococcus
• Enteric bacilli (Escherichia coli, Proteus, Klebsiella)
• Listeria (also seen in the elderly)
Meningitis in children and adults
• Haemophilus influenzae
• Neisseria meningitidis (or meningococcus)
• Streptococcus pneumoniae (or pneumococcus)
Less common meningitides
• Staphylococcus
• Pseudomonas
• Gram-negative meningitis
• Tuberculous meningitis
• Neurosyphilis
Brain abscess
• Staphylococci
• Norcardia
Changes in protein and glucose content of CSF often accompany

an increase in cellularity (Table 9.3):
●● Neutrophilic pleocytosis. This is seen in bacterial, early viral,
tuberculous and fungal meningitis, cerebral abscesses, CNS

hemorrhage, cerebral infarct, and high-grade malignancy (tumor
necrosis).
●● Lymphocytic pleocytosis (Fig. 9.4). This is seen in aseptic, viral,
tuberculous, or fungal meningitis, partially treated bacterial

meningitis, parasitic disease, polyneuritis, and Guillain–Barre
syndrome. (Table 9.4) The CSF sample usually contains numer-
ous monomorphic small lymphocytes. The differential diag-
nosis includes reactive lymphocytosis vs. small lymphocytic
lymphoma (rarely seen in the CSF). An adequate history and/or
flow cytometry will help resolve this differential diagnosis.
●● Monocytic pleocytosis. This is seen in patients with viral menin-
goencephalitis, Mollaret meningitis, tuberculosis, neurosyphilis,

amebic infections, fungal disease, as well as multiple sclerosis
and reactions to foreign material.
Central Nervous System Infections 207
Table 9.2. Common causes of CSF pleocytosis.

Neutrophilic pleocytosis
• Bacterial infection
• Early viral infection
• Tuberculosis infection
• Fungal meningitis
• Cerebral abscess
• CNS hemorrhage
• Cerebral infarct
• High-grade malignancy
Lymphocytic pleocytosis
• Viral (aseptic) meningitis
• Tuberculosis meningitis
• Partially treated bacterial meningitis
• Parasitic disease
• Polyneuritis
• Guillain–Barre syndrome
Monocytic pleocytosis
• Tuberculosis infection
• Syphilis infection
• Amebic infection
• Fungal infection
• Viral meningoencephalitis
• Multiple sclerosis
• Reaction to foreign material
Eosinophilic pleocytosis
• Parasitic infection
• Fungal infection
• Foreign material reaction (drugs, shunts)
• Idiopathic conditions
• Acute polyneuritis
• Meningioencephalitis (bacterial, viral, and fungal)
• Lymphoma
• Primary brain tumors
●● Eosinophilic pleocytosis. This is seen in parasitic and fungal

infections, reactions to foreign material (shunts) and drug
induced or idiopathic conditions, acute polyneuritis, infections
(bacterial, viral, and fungal meningoencephalitis), lymphoma,
as well as primary brain tumors.
208
Table 9.3. CSF parameters with various infections.

9.
Condition Color Glucose Protein Leukocytes

Normal Clear and colorless 50–80 mg/dL 20–45 mg/dL Fewer than six lymphocytes,
no neutrophils
Bacterial meningitis Cloudy Low to very low High Markedly increased neutrophils
to very high
Viral meningitis Clear to cloudy Normal High Increased lymphocytes and monocytes
Fungal meningitis Clear to cloudy Low High Variable from no inflammation to
increased neutrophils and/or
lymphocytes
Tuberculous meningitis Clear to cloudy Low High Increased neutrophils early, increased
lymphocytes and monocytes later
Neurosyphilis Clear to cloudy Normal High Increased lymphocytes and monocytes
and/or plasma cells
Central Nervous System Infections
Parasitic meningitis Clear to cloudy Low or normal High Normal or increased neutrophils,
eosinophils, lymphocytes and/or
monocytes
Intracranial hemorrhage Clear to pink-red to Normal to low High Normal or increased neutrophils and/or
xanthochromic (yellow-orange) lymphocytes
Neoplastic Clear to cloudy, pink-red or Normal to low Normal Normal or increased neutrophils and/or
xanthochromic if associated to increased lymphocytes
with hemorrhage
Acute Bacterial Meningitis 209
Table 9.4. Common causes of lymphocytic meningitis.

• Viral meningitis or encephalitis
• Partially treated purulent meningitis
• Tuberculous meningitis
• Listeria meningitis
• Brucella meningitis
• Syphilitic meningitis
• Lyme disease
• Sarcoidosis
• Various protozoal or helminthic infections
• Lymphoma
• Demyelinating disease
• Vascular disease (vasculitis, stroke, subarachnoid hemorrhage)
There are a variety of ancillary tests that can be performed on

CSF to help make a diagnosis of infection such as protein and glu-
cose levels, special stains (e.g., Gram stain, India ink preparation),
culture and sensitivity, serology for antigens and antibodies (e.g.,
Venereal Disease Research Laboratory test or VDRL test for neu-
rosyphilis), and detection of viral genetic material (DNA, RNA) by
PCR. The presence of an increase of antibodies over time indicates
a recent infection.
Acute Bacterial Meningitis

Microbiology
●● The etiology varies with age. Neisseria meningitidis infection
is most common in childhood, Haemophilus influenzae com-
monly affects children under 5 years of age (and may rarely be
seen due to vaccination) and Streptococcus pneumoniae affects
individuals of all ages. In the elderly and infants, the diagnosis
may be challenging.
●● Bacteria can reach the subarachnoid space via the bloodstream or by
extension from contiguous structures such as the sinuses or ears.
●● Bacterial infection usually affects the subarachnoid space. How-
ever, toxins (from bacteria or leukocytes) can cause edema and
damage blood vessels, causing additional cellular damage. Cere-
bral edema causes an increase in intracranial pressure (Fig. 9.1).
Fig. 9.1. Acute bacterial meningitis. The cytospin shows marked neutrophils
(PMNs) and cellular debris. Some lymphocytes and monocytes are also
present (Diff-Quik stain, intermediate magnification, left and high magnifica-
tion right). The Gram stain (inset) shows intracellular Gram negative bacilli
Clinical Features
●● The classic clinical trial of acute meningitis is fever, mening-
ismus (stiff neck resistant to flexion), and a change in mental
status.
●● The cytologic features include CSF with a marked pleocytosis
(particularly neutrophils), cloudy turbid appearance, fibrin, and
cellular debris.
●● Very early disease may show very few cells or a predominance
of lymphocytes.
●● Occasionally intracellular bacteria may be identified.
Acute Bacterial Meningitis 211
Fig. 9.2. This cerebrospinal fluid (CSF) is from a 73 year old male with
no prior history of malignancy. His CSF specimen shows numerous neu-
trophils with very rare large atypical cells (see circle, right) suspicious for
carcinoma (Diff-Quik stain; low magnification, left; and high magnifica-
tion, right). On follow up of this case, the patient was found to have a large
neuroendocrine carcinoma of the colon.
●● Early viral meningitis/encephalitis
●● Brain, subdural, and epidural abscess
●● Tuberculosis meningitis
●● Fungal infection
●● Traumatic tap
●● Toxoplasmosis
●● Brain tumor. Some high-grade brain tumors may show marked
necrosis and increased neutrophils, due to a paraneoplastic syn-
drome. Therefore, cases with neutrophilic pleocytosis should be
screened carefully for any atypical cells to exclude a neoplastic
process (Fig. 9.2)
●● Leukemia
Ancillary Studies
●● Gram stain
●● High protein levels in CSF
●● Low CSF glucose level (less than 50% of the serum level)
●● Microbiology bacterial culture (aerobic and anaerobic)
●● Bacterial antigens in CSF offer rapid testing
●● Molecular testing: PCR assays for specific organisms; amplifi-
cation of 16S rRNA gene; and ribosomal DNA assay
Viral Meningitis
Microbiology
●● Viral meningitis is also called “aseptic meningitis,” since there
are no bacteria grown on culture.
●● Early HIV infection (at the initial seroconversion stage) may
present as aseptic meningitis.
Clinical Features
●● Patients present with the clinical trial of acute meningitis that
includes fever, meningismus (stiff neck resistant to flexion), and
a change in mental status. They typically have no focal neuro-
logical disease or seizures.
●● CSF is usually under normal pressure and contains a moder-
ate number of white blood cells (<500/mm3). CSF may show a
marked pleocytosis for weeks.
●● The CSF initially may contain predominantly neutrophils
(PMNs), but after a day or two shows lymphocytosis.
●● CSF protein and glucose are within normal range or may show
minimal changes.
●● Viral meningitis is usually a self-limited disease and complica-
tions are infrequent (Fig. 9.3).
●● CSF is hypercellular with a predominance of lymphocytes.
●● Some atypical immature lymphocytes may be seen. Flow cytom-
etry may be necessary in such cases to exclude lymphoma.
Viral Meningitis 213
Fig. 9.3. This CSF is from a patient with viral meningitis showing marked
lymphocytosis. The CSF specimen shows numerous mature lymphocytes.
The microbiology cultures were negative (Diff-Quik stain, low magnifica-
tion left, and high magnification right).
●● There is no necrosis or cellular debris and bacteria are not

found.
●● Viral inclusions are rarely identified in CSF.
●● Bacterial meningitis (late stage or partially treated)
●● Lyme disease (comprised of polytypic B-cells)
●● Brain abscess
●● Parameningeal sepsis
Ancillary Studies
●● Stains for bacteria (Gram) and mycobacteria are negative
●● Glucose is normal and protein levels may be slightly high or
normal
●● Viral cultures can be performed
Fig. 9.4. Reactive lymphocytosis. CSF with a lymphocytic pleocytosis.

This CSF specimen shows numerous lymphocytes including immature
forms (Pap stain, intermediate magnification, left; and high magnifica-
tion, right). It was initially considered suspicious for lymphoma. Flow
cytometry was negative for lymphoma and the follow up in this patient
showed no evidence of malignancy. Subsequent CSF showed a decrease
in cellularity and return to normal.
●● PCR testing for specific viruses (such as enterovirus, HSV,

CMV, HIV)
●● The intensity of lymphocytosis (leukemoid reaction) and the
presence of immature or atypical appearing lymphocytes
may cause an erroneous diagnosis of leukemia or lymphoma
(Fig. 9.4). Flow cytometry is recommended in these conditions
Mollaret Meningitis
Microbiology
●● This is a rare form of recurrent, aseptic, chronic meningitis that
may be related to Herpes simplex type 1 and 2 or West Nile
virus infection.
Mollaret Meningitis 215
Fig. 9.5. CSF from a 31 year old female with chronic Mollaret meningitis.
The specimen shows marked monocytosis present in a background of
scant mature lymphocytes. Monocytes exhibit a variety of nuclear mor-
phologies (see circles) including bean shaped and bilobed nuclei, as well
as cells with nuclear clefting and cerebriform nuclear contours (Diff-Quik
stain, intermediate magnification, left; and high magnification, right).
Clinical Features
●● Meningitis is usually mild and self-limiting. Patients experience
recurrent episodes of headache, fever, and photophobia sepa-
rated by symptom-free episodes.
●● CSF shows marked monocytosis with characteristic Mollaret
cells (activated monocytes).
●● Mollaret cells are somewhat bean shaped, have enlarged nuclei
and cerebriform nuclei with deep nuclear clefts, leading to their
characteristic “footprint” appearance. These cells are usually
seen within the first 24 h of the onset of symptoms.
●● There are often background lymphocytes and some degenerated
monocytes (“ghost cells”) present (Fig. 9.5).
●● Other inflammatory and infectious diseases of the CNS
●● Lymphoproliferative disorder
Ancillary Studies
●● PCR assays for viral agents such as HSV-2 or West Nile virus
(not all cases test positive)
Tuberculous Meningitis
Microbiology
●● Meningitis caused by Mycobacterium tuberculosis usually
results from seeding of a tuberculoma (benign mass caused
by tuberculosis) in the brain or meninges. Tuberculomas arise
largely as a result of hematogenous spread from distant disease
(typically in the lung) (Fig. 9.6).
Clinical Features
●● Children, debilitated and immune incompetent adults are at
greatest risk for TB meningitis.
●● Infected patients present with a headache, malaise, fever, and
weight loss.
●● The level of CSF protein is high and glucose is low.
●● CSF shows a moderate pleocytosis with a predominance of
lymphocytes.
●● Bacterial meningitis
●● Fungal meningitis
●● Lyme disease
●● Brain abscess
Cryptococcal Meningitis 217
Fig. 9.6. TB meningitis. This CSF specimen from a 2-month-old male

infant shows numerous neutrophils and lymphocytes, as well as some
monocytes (Pap stain, high magnification, right and lower magnification,
left). Microbiology culture confirmed Mycobacterium tuberculosis. The
upper right inset shows a higher magnification of the polymorphous lym-
phocytes seen in this case.
Ancillary Studies
●● AFB stain, which is only occasionally positive (low sensitivity)
●● Culture for mycobacteria (takes 2–8 weeks to grow)
●● Chest X-ray, sputum, skull X-ray, and a tuberculin test may indi-
cate a distant source of infection
●● PCR for diagnostic confirmation and typing
Cryptococcal Meningitis
Microbiology
●● Meningitis occurs following CNS infection by the fungus Cryp-
tococcus neoformans, and less of C. gattii.
●● Cryptococcus is the most common mycosis of the CNS.
Fig. 9.7. Cryptococcal meningitis. This CSF specimen shows numerous

pink/red round yeasts with thick capsules and narrow-based, asymmetric
budding, highlighted in the upper right inset (Pap stain, high magnifica-
tion). Note that there is an absence of an inflammatory reaction in the
background.
Clinical Features
●● Meningitis may occur in healthy and immunocompromised
patients. Predisposing factors include a debilitated state, immune
incompetence, and diabetes mellitus.
●● Infection is indolent and symptoms may extend over a long
period before the diagnosis is confirmed.
●● Symptoms include headache and mental deterioration. Other
symptoms may include cranial nerve palsies and focal brain
stem dysfunction secondary to arteritis (Fig. 9.7).
●● Cryptococcal yeast may be variable in number, ranging from rare
to abundant organisms. Yeast (5–15 mm) are round, but can be
indented and trap air under the coverslip, resulting in a crystal-
like refractile artifact. They are pink or purple with a Pap stain.
Blastomycosis 219
●● Budding is narrow-based and asymmetric.

●● Typically there are no associated inflammatory cells. However,
one may also encounter a granulomatous response or vari-
able inflammatory background composed of lymphocytes and
monocytes. Organisms are harder to find when there are many
inflammatory cells present.
●● Other fungal microorganisms
●● Mimics of fungus (such as talc)
Ancillary Studies
●● GMS and PAS stains
●● Mucicarmine stain to demonstrate mucin-positive capsules
●● India ink (requires a fresh specimen)
●● CSF antigen test
●● Immunocytochemistry using a specific antibody to C. neoformans
Blastomycosis
Microbiology
●● Blastomycosis is a chronic systemic fungal infection due to
Blastomyces dermatitidis that characteristically affects the skin
and lungs.
●● Involvement of the CSF (meningitis) or other CNS location
(intracranial mass lesion) is rare. Approximately 2.5% of patients
with pulmonary or systemic blastomycosis develop CNS
involvement (Fig. 9.8).
Clinical Features
●● Patients may present with clinical features typical of meningitis
or with signs and symptoms related to a brain mass.
●● The CSF protein level is usually elevated and CSF glucose level
typically normal or decreased.
Fig. 9.8. Blastomycosis. The radiology image (upper left) from a 52-year-old
man shows a large posterior cerebellar brain mass due to blastomyco-
sis infection destroying the skull bone. The Pap stained imprint cytology
specimen shows numerous large budding yeasts (right image), with broad
based buds (middle left). A GMS stain is positive (bottom left). A brain
biopsy confirmed blastomycosis infection. All images are shown with
high magnification (images courtesy of Dr. Pawel Schubert, University of
Stellenbosch, Cape Town, South Africa).
●● There is a CSF pleocytosis which may demonstrate a lymphocytic
or neutrophilic predominance. Patients may also present with
granulomatous meningitis.
●● The finding of large (8–15 mm) budding yeasts with broad based
buds is necessary to help establish the diagnosis. Yeasts are usu-
ally found within macrophages.
●● Other fungal microorganisms
●● Neoplastic lesions in the case of a brain mass
●● Mimics of fungus (such as talc)
Brain Abscess 221
Ancillary Studies
●● Microbiology culture. This has low sensitivity for CSF obtained
via lumbar puncture. However, culture of ventricular fluid is
associated with greater sensitivity.
Brain Abscess
Microbiology
●● Bacteria are the most common organisms recovered from cultures
of brain abscesses, including Streptococcus cocci, Pseudomonas,
Neisseria, Haemophilus, Nocardia, and Mycobacterium. Most
brain abscesses are caused by infections with mixed flora.
●● Other organisms that may cause a brain abscess include fungi
and parasites (e.g., Toxoplasma gondii, amebae), especially in
immunocompromised patients.
●● The source of a brain abscess may be a local (skull fracture,
ear, dental, paranasal sinuses, epidural) or remote (lung, heart,
etc.) infection. Spread of microorganisms is by hematogenous
or direct extension.
●● Aerobic bacteria are frequently cultured from abscesses that
have sinus tracts connecting them to the exterior, such as
middle-ear infections and skull fractures. On the other hand,
areas in the brain with ischemic injury are most likely to include
anaerobic or microaerophilic organisms.
Clinical Features
●● Patients may experience symptoms related to increased intracra-
nial pressure (e.g., headache, vomiting, confusion, coma), infec-
tion (e.g., fever) and focal tissue damage (e.g., palsy).
●● An untreated brain abscess may cause cerebral herniation or
rupture into the ventricles, causing severe fatal meningitis.
●● Examination of the CSF shows no abnormalities or may be sim-
ilar to acute bacterial meningitis.
●● Stereotactic biopsy may occasionally be required for the

diagnosis. Procured abscess material includes many neutrophils
and associated cellular debris.
●● Bacterial meningitis
●● Tuberculosis meningitis
●● Brain tumor with acute inflammation
●● Leukemia
Ancillary Studies
●● Gram stain for bacteria
●● GMS and PAS stain for fungi
●● Acid-fast stain for mycobacteria and Norcardia
●● Immunocytochemistry for specific microorganisms (e.g.,
Toxoplasma)
Shunt Infections
Microbiology
●● Ventriculoperitoneal (VP) shunts are used for intracranial
pressure management and temporary CSF drainage.
●● An Ommaya reservoir is an intraventricular catheter system used
for the aspiration of CSF or for intrathecal delivery of drugs
(e.g., chemotherapy for brain tumors) into the CSF.
●● These foreign devices may introduce infections into the CNS.
Typical infections are caused by bacteria (e.g., Staphylococ-
cus epidermidis, S. aureus, Acinetobacter spp.) and rarely from
fungi (e.g., Candida spp.). Shunts terminating in the perito-
neal cavity have a greater risk of infection with Gram-negative
organisms.
●● In patients with infected ventricular shunts, cultures of CSF
from the shunt or ventricles are more likely to be positive than
CSF obtained via lumbar puncture.
Neurosyphilis 223
Clinical Features
●● Infection of the CNS is a major cause of morbidity and mortality
in patients with CSF shunts. They may cause seizures and shunt
malfunction.
●● CSF shows a pleocytosis and depending on the chronicity of
infection will have a lymphocytic or neutrophilic predomi-
nance.
●● Microorganisms (e.g., bacteria, Candida) may be observed.
Intracellular organisms are indicative of true infection, and not
just colonization.
●● Leukemoid reaction
●● Brain tumor with inflammation
Ancillary Studies
●● Special stains (Gram, GMS and PAS) for microorganisms
Neurosyphilis
Microbiology
●● Neurosyphilis is caused by infection with the spirochetal bacte-
rium Treponema pallidum.
Clinical Features
●● Syphilis can produce a variety of CNS disorders which may
mimic other infections as well as vascular, neoplastic, or degen-
erative disease.
●● The most common presentation of neurosyphilis is meningitis
(28%), followed by systemic features and dementia.
Fig. 9.9. Neurosyphilis. This CSF specimen from a 48 year old HIV posi-
tive male shows numerous lymphocytes and plasma cells (Diff-Quik stain,
Intermediate magnification, left; and high magnification, right). Serologi-
cal testing supported a diagnosis of neurosyphilis.
●● Meningitis may occur within 5 years of a person first contracting

this infection. From 7 to 15 years after contact, inflammatory
meningovascular syphilis can produce brain infarction in any
area of the CNS. Tertiary syphilis (15–20 years after contact)
has two classic presentations: tabes dorsalis (spinal cord degen-
eration) and paretic neurosyphilis (general paresis) (Fig. 9.9).
●● The cytological features of neurosyphilis are nonspecific, and
include pleocytosis with a marked increase in lymphocytes and
plasma cells.
●● Other infectious agents
●● Other conditions with increased plasma cells such as plasma
cell neoplasia, late bacterial infection, and multiple sclerosis
Toxoplasmosis 225
Ancillary Studies
●● CSF chemistry (high protein level and positive IgG oligoclonal
bands)
●● Serology using (1) nonspecific (reagin) tests such as rapid plasma
reagin (RPR) or the VDRL, or (2) specific treponemal antibody
tests such as the fluorescent treponemal antibody (FTA) test.
A false positive CSF VDRL occurs only when positive blood
is inadvertently introduced into the CSF by a traumatic lumbar
puncture. Occasionally all these tests are negative.
Toxoplasmosis
Microbiology
●● Toxoplasmosis is caused by infection with the obligate intracel-
lular protozoal parasite T. gondii.
●● Ingested oocysts transform into tachyzoites which localize in
neural and muscle tissue where they subsequently develop into
tissue cyst bradyzoites (Fig. 9.10).
Clinical Features
●● In the CNS, toxoplasmosis may present with meningoencepha-
litis or with multiple small abscesses.
●● Toxoplasmosis infection is more common in immunosuppressed
persons, and is a common opportunistic infection in AIDS
patients. It is the most common cause of a focal brain lesion in
patients with AIDS.
●● Congenital infection may cause underdevelopment of the cer-
ebrum resulting in microcephaly and mental retardation.
●● Ocular disease from Toxoplasma infection can result from con-
genital infection or infection after birth.
●● CSF in these cases shows neutrophils mixed with mononuclear
cells, and only rarely tachyzoites.
●● In cytology specimens from brain lesions, microorganisms are
usually sparse. Typical cysts containing oval- or crescent -shaped
Fig. 9.10. Toxoplasmosis infection. These images are from imprint cytol-
ogy of a brain biopsy in an HIV + man. (Left) A small oval cyst with
intracellular parasites is shown (arrow) as well as several small scattered
parasites (circles) in the background (Pap stain, high magnification).
(Right) An immunostain confirms the presence of toxoplasmosis (high
magnification).
bradyzoites are best seen in air-dried Romanowsky stained (e.g.,

Diff-Quik) preparations. The background contains associated
abundant macrophages, polymorphous lymphoid cells, and
occasional reactive astrocytosis.
●● Cerebral vasculitis
●● CNS lymphoma
●● HIV encephalopathy
●● HIV dementia
●● Other (non-HIV) forms of dementia
●● Cerebrovascular disease
●● Neurosyphilis
Neurocysticercosis 227
Ancillary Studies
●● Special stains (Giemsa stain)
●● Immunocytochemistry using antibodies for T. gondii
●● Serology
Neurocysticercosis
Microbiology
●● Neurocysticercosis is an infection of the brain or spinal cord due
to the pork tapeworm Taenia solium.
●● In the CNS, larvae cannot grow to adult worms. Hence, they
remain as cysts indefinitely. When they die the cyst ruptures
which evokes an inflammatory response.
●● T. solium is the most common helminthic infestation to affect
the CNS worldwide.
Clinical Features
●● Patients may present with seizures.
●● Imaging studies typically reveal a focal brain lesion.
●● CSF contains abundant eosinophils, as well as mononuclear
cells.
●● Larvae are not identified.
●● Angiostrongyliasis
●● Schistosomiasis
●● Other causes of CSF eosinophilic pleocytosis
Ancillary Studies
●● Serology
Primary Amebic Meningoencephalitis

Microbiology
●● Primary amebic meningoencephalitis (PAM) is caused by infec-
tion from Naegleria fowleri.
●● These parasites live in warm, unchlorinated, stagnant bodies of
freshwater. While swimming, infection is acquired through the
nose, typically during the summer months. The parasites then
rapidly spread into the CNS.
Clinical Features
●● Patients may manifest with encephalitis and experience headache,
nausea, vomiting, neck rigidity, seizures, and eventually coma.
●● Death usually occurs within 14 days of exposure when the infec-
tion spreads to the brain stem.
●● Non-encapsulated ameba can be identified in CSF. They have a
relatively large nucleus and little cytoplasm.
●● CSF reveals a neutrophilic pleocytosis with early infection, and
a predominant mononuclear leukocytosis with more chronic
infection.
●● Ameba may be hard to differentiate from mononuclear cells.
●● Amebic brain abscess due to Entamoeba histolytica. These amebae
are not seen in CSF.
Ancillary Studies
●● Wet preparation to identify microorganism motility
●● Serology (rising titers)
Angiostrongyliasis 229
Angiostrongyliasis
Microbiology
●● Angiostrongyliasis is an infection by a nematode from the Angi-
ostrongylus genus, usually from the lungworm Angiostrongylus
cantonensis acquired after consuming certain molluscs.
●● Circulating larvae migrate to the meninges where they may
develop into the adult form in the brain and CSF. However, they
soon die and incite an inflammatory reaction.
●● It is the most common cause of eosiniphilic meningitis.
Clinical Features
●● Patients are usually from or have traveled recently to the South
Pacific, Hawaii, or the Caribbean.
●● Patients usually present with a headache, and occasionally neck
stiffness and mild cognitive impairment.
●● Infection may resolve without treatment, but with a heavy load
of parasites there may be severe symptoms (paresis, coma), per-
manent CNS sequelae, or even death.
●● Unlike cysticercosis, focal brain lesions are not identified by
imaging studies.
●● CSF typically shows a marked eosinophilic pleocytosis (greater
than 10% eosinophils).
●● Larvae are only rarely identified in CSF, especially in pediatric
patients.
●● Neurocysticercosis
●● Other roundworm infections that present with eosinophilic men-
ingitis (Gnathostoma spinigerum, Baylisascaris procyonis)
●● Other causes of CSF eosinophilic pleocytosis
Ancillary Studies
●● Serology (tests are not widely available)
Suggested Reading
Brogi E, Cibas ES. Cytologic detection of Toxoplasma gondii tachyzoites
in cerebrospinal fluid. Am J Clin Pathol. 2000;114:951–5.
Cajulis RS, Hayden R, Frias-Hidvegi D, Brody BA, Yu GH, Levy R. Role
of cytology in the intraoperative diagnosis of HIV-positive patients
undergoing stereotactic brain biopsy. Acta Cytol. 1997;41:481–6.
Chan TY, Parwani AV, Levi AW, Ali SZ. Mollaret’s meningitis: cytopatho-
logic analysis of fourteen cases. Diagn Cytopathol. 2003;28:227–31.
Garges HP, Moody MA, Cotten CM, Smith PB, Tiffany KF, Lenfestey R,
et al. Neonatal meningitis: what is the correlation among cerebrospinal
fluid cultures, blood cultures, and cerebrospinal fluid parameters? Pedi-
atrics. 2006;117:1094–100.
Gupta PK, Gupta PC, Roy S, Banerji AK. Herpes simplex encephalitis,
cerebrospinal fluid cytology studies. Two case reports. Acta Cytol.
1972;16:563–5.
Silverman JF. Cytopathology of fine-needle aspiration biopsy of the brain
and spinal cord. Diagn Cytopathol. 1986;2:312–9.
Teot LA, Sexton CW. Mollaret’s meningitis: case report with immunocy-
tochemical and polymerase chain reaction amplification studies. Diagn
Cytopathol. 1996;15:345–8.
van de Beek D, de Gans J, Tunkel AR, Wijdicks EF. Community-acquired
bacterial meningitis in adults. N Engl J Med. 2006;354:44–53.
Verstrepen WA, Bruynseels P, Mertens AH. Evaluation of a rapid real-
time RT-PCR assay for detection of enterovirus RNA in cerebrospinal
fluid specimens. J Clin Virol. 2002;25 Suppl 1:S39–43.
Weller PF, Liu LX. Eosinophilic meningitis. Semin Neurol. 1993;
13:161–8.
10
Hematologic Infections
Sara E. Monaco, Walid E. Khalbuss,
and Liron Pantanowitz
Fine needle aspiration (FNA) biopsy is a rapid, safe, accurate, and

cost-effective diagnostic technique that has proven to success-
fully diagnose hematologic infections and guide treatment deci-
sions. The cytomorphologic findings of hematologic infections
show several patterns (Table 10.1). Hematologic infections that
manifest with lymphadenopathy and/or splenomegaly may mimic
lymphoma. Hence, apart from obtaining a pathologic diagnosis,
cytology specimens from nodes or spleen should be triaged for
lymphoma work up (e.g., flow cytometry), microbiology culture
in a sterile container, and other special studies (e.g., PCR). This
chapter highlights key hematologic infections and focuses on their
cytomorphology, differential diagnosis, and ancillary studies.
Lymph Node Infections

Acute Suppurative Lymphadenitis
●● This form of lymphadenitis is characterized by acute inflamma-
tion and possible abscess formation with pus. Typical infectious
causes include pyogenic bacterial organisms (e.g., Staphylo-
coccus, Streptococcus spp., Gram-negative bacilli), less likely
actinomycetes (Actinomyces and Nocardia spp.) and some
fungi (Candida, Aspergillus, Zygomycetes).

232
10.
Table 10.1. Cytomorphologic patterns of hematologic infections.

Characteristic Heterogeneous Suppurative Granulomatous Homogeneous
feature lymphocytes lymphadenitis inflammation Necrosis lymphocytes
Predominant Small polymorphous Neutrophils Macrophages None Atypical monotonous
cell type lymphocytes lymphocytes
Background Lymphoglandular Inflammatory debris ±Inflammatory or Necrotic debris Lymphoglandular
bodies necrotic debris bodies
Macrophages Tingible body Few Many epithelioid Few Tingible body
macrophages or spindle histiocytes macrophages
Hematologic Infections
Infectious Viral, early bacterial, Bacteria, early cat Tuberculosis, Mycobacteria, EBV (infectious
etiology or early cat scratch scratch, tuberculosis, tuberculoid leprosy, fungi mononucleosis),
infection atypical mycobacteria, fungi, atypical toxoplasmosis
actinomyces, fungi, HSV, mycobacteria, cat
pneumocystis scratch, LGV,
leishmania
Noninfectious Reactive lymphoid Kikuchi’s, SLE-related Foreign body, Metastatic tumor, Lymphoma
etiology hyperplasia, lymphadenopathy, sarcoidosis, infarction
dermatopathic infarction malignancy,
lymphadenitis, lipogranulomas
low-grade lymphoma
Lymph Node Infections 233
Fig. 10.1. Acute suppurative lymphadentitis (Pap stain, high magnifica-

tion). This lymph node FNA shows numerous neutrophils in a background
of granular inflammatory debris.
●● Clinically, patients may manifest with pyrexia and enlarged,

tender localized superficial lymph nodes (neck, axilla, groin)
(Fig. 10.1).
●● Gross shows purulent aspirated material.
●● Predominance of neutrophils and inflammatory debris.
●● Careful examination may reveal intracellular and extracellular
organisms.
●● Abscess
●● Cat Scratch disease
●● Lymphogranuloma venereum
●● Tularemia
234 10. Hematologic Infections
●● Kikuchi’s lymphadenitis where karyorrhectic debris mimics

neutrophils
●● Inflammatory cysts (e.g., infected branchial cleft cyst)
●● Metastatic tumor with superimposed acute inflammation
Ancillary Studies
●● Special stains and immunostains for organisms
Cat Scratch Lymphadenitis

●● This acute self-limited acute necrotizing granulomatous lym-
phadenitis is caused by infection with the Gram-negative bacil-
lus Bartonella henselae, and less often Bartonella quintana.
●● Infected patients typically develop regional (localized) lym-
phadenopathy 1–3 weeks after a bite or scratch on the nearby
skin from a cat. Low-grade fever can occur in one third of
patients. Rare cases may develop more severe systemic disease
(e.g., hepatosplenomegaly).
●● Lymphadenopathy has three stages. The initial phase is char-
acterized by florid reactive lymphoid hyperplasia. The second
phase has loose granulomas and single histiocytes. A late phase
(most characteristic) has both acute suppurative and palisading
granulomatous lymphadenitis (Fig. 10.2).
●● Aspirates contain a variable amount of acute suppurative or
granulomatous inflammatory material. Macrophages may form
tight granulomas, dispersed epithelioid histiocytes, or present as
suppurative granulomas.
●● Bacteria are only rarely identified without special stains.
●● Necrotizing granulomatous inflammation in Mycobacterial or
fungal infection
●● Acute suppurative lymphadenitis and abscess, which usually
lack granulomas
Fig. 10.2. Cat scratch lymphadentitis (Pap stain, high magnification;

inset: Immunostain for Bartonella henselae, high magnification). FNA of
this lymph node shows granulomatous inflammation with characteristics
of acute suppurative granulomatous lymphadenitis seen in cat scratch dis-
ease. Pleomorphic bacteria are best highlighted using immunocytochem-
istry with a monoclonal antibody to B. henselae (inset).
●● Tularemia
●● Lymphogranuloma venereum
Ancillary Studies
●● B. henselae form pleomorphic aggregates of bacilli that do not
stain well with a Gram stain. Therefore, a modified silver stain
(modified Steiner stain or Warthin-Starry stain) can be used for
their identification. Silver positive organisms may be hard to
distinguish from stained background debris.
●● Immunocytochemistry with a monoclonal antibody to B. henselae.
Immunostains are more widely available, cost-effective, and
faster than molecular studies. This is the best way to identify
B. henselae, but the antibody will not detect other strains of
Bartonella.
●● PCR or Southern blot for B. henselae. PCR is more sensitive

than special stains.
●● Serologic studies are of low sensitivity and specificity because
some patients may never have a detectable antibody response.
●● Microbiology culture, although this is a difficult and lengthy
(9–45 days) procedure due to the slow growth of the organism.
Lymphogranuloma Venereum
●● This sexually transmitted disease is caused by infection with
Chlamydia trachomatis, an obligate intracellular organism.
●● Clinically, patients may present with a painless ulcer at the
mucosal site of entry about 7–12 days after sexual contact. Lym-
phadenopathy (buboes) follows 1–8 weeks later. Infected lymph
nodes are usually tender and mobile, but matted nodes and sinus
tracts can also occur.
●● FNA of involved nodes yield neutrophils, other inflammatory
cells (plasma cells, lymphocytes), macrophages, and occasional
multinucleated giant cells, as well as necrosis.
●● Microorganisms are not readily identified without special stains.
●● Acute suppurative lymphadenitis
●● Cat Scratch disease
●● Tularemia
●● Kikuchi’s lymphadenitis
Ancillary Studies
●● Special stains can be helpful. The organisms are Gram-negative
and can be identified with a Warthin-Starry stain.
●● Electron microscopy
●● PCR for the 16S ribosomal DNA
●● Complement fixation and serologic testing
Fig. 10.3. Non-necrotizing granulomatous inflammation (Diff-Quik

stain, high magnification). FNA of a lymph node contains discrete non-
necrotizing granulomas in a patient with a clinical history of sarcoidosis.
Granulomatous Lymphadenitis
●● This type of chronic inflammation within a lymph node is com-
posed of aggregates of epithelioid macrophages (granulomas).
●● Granulomas can occur as a result of infectious processes (e.g.,
tuberculosis, fungal infection) or noninfectious processes
(e.g., sarcoidosis, foreign body reaction), and with certain
malignancies (Figs. 10.3 and 10.4).
●● Granulomas are characterized by clusters of epithelioid mac-
rophages. Reactive histiocytes have elongated, kidney bean or
boomerang-shaped vesicular nuclei with nucleoli, abundant
granular cytoplasm (eosinophilic on H&E and cyanophilic on
Pap stain), and ill-defined cytoplasmic cell borders sometimes
resulting in syncytial formation.
Fig. 10.4. Necrotizing granulomatous inflammation (Pap stain, low

agnification). An aggregate of epithelioid histiocytes occurs within a
m
background of granular necrotic debris in this case of tuberculosis.
●● Three morphologic patterns may be encountered including

suppurative, necrotizing, and non-necrotizing granulomatous
inflammation (Table 10.2).
●● There may be intermixed lymphocytes, plasma cells, occasion-
ally multinucleated giant cells, and neutrophils present depend-
ing on the aforementioned inflammatory pattern.
●● Close examination may identify an associated microorganism.
●● Suppurative granulomatous inflammation may occur with
dimorphic fungi (Blastomyces, Coccidioides, Paracoccidioides,
Chromoblastomycosis and Phaeohyphomycosis, Sporotrichosis).
●● Granulomas may be associated with malignancy (e.g.,
lymphoma, squamous cell carcinoma, seminoma).
●● Mimics: Lymphohistiocytic aggregates in reactive lymphoid
hyperplasia, sinus histiocytosis, dendritic cells, low-grade
neoplasms (Table 10.2).
Table 10.2. Different patterns of granulomatous lymphadenitis.
Features Acute suppurative granulomas Necrotizing granulomas Non-necrotizing granulomas
Predominant cell type Neutrophils and epithelioid Epithelioid histiocytes Epithelioid histiocytes
histiocytes
Background Inflammatory or necrotic debris Necrotic debris Clean
Infection Bacteria, cat scratch disease, Tuberculosis, fungi, cat scratch Atypical mycobacteria, histoplasmosis,
tuberculosis, herpes simplex virus, disease leishmaniasis, schistosomiasis
dimorphic fungi
Noninfectious etiology Immunodeficiency, lymph node Kikuchi lymphadenitis, Sarcoidosis, foreign-body, lipogranu-
infarction lymph node infarction lomas, lymphoma, metastatic
tumor (seminoma, squamous cell
carcinoma)
Lymph Node Infections
239
Ancillary Studies
●● Special stains for mycobacteria (acid-fast bacilli [AFB]) and
fungi (Grocott, periodic acid-Schiff [PAS]) should be routinely
performed to exclude an infectious etiology.
●● Immunostains with S-100 and CD68 (KP1) can be used to con-
firm the presence of macrophages.
●● Polarization microscopy to exclude foreign polarizable material.
Mycobacterial Lymphadenitis
●● Lymphadenitis may be caused by infection with Mycobacterium
tuberculosis (TB) or nontuberculous (atypical) mycobacteria
such as Mycobacterium avium-intracellulare (MAI) belonging
to the group Mycobacterium avium complex (MAC).
●● Tuberculous lymphadenitis is the most common form of myco-
bacterial lymphadenitis in the world, and the most common
extrapulmonary manifestation of TB, predominantly in less
developed countries.
●● Individuals at risk for mycobacterial infection are young children,
elderly adults, and those who are immunosuppressed (e.g.,
human immunodeficiency virus [HIV]-positive patients).
●● In general, FNA detects around half of the cases of mycobacterial
lymphadenitis and has a high specificity and positive predictive
value. However, there is a high false negative rate due to the
absence of typical granulomas and/or necrosis in cases of early
tuberculous lymphadenitis. A combination of test modalities
including staining for AFB and PCR can optimize sensitivity
and specificity (Fig. 10.5).
●● Granulomas are composed of clusters of benign epithelioid
histiocytes that may be mixed with lymphocytes.
●● Tuberculous lymphadenitis has granulomas with Langhans
and/or foreign body-type multinucleated giant cells present in
a necrotic background. Mycobacteria are sparse and usually
difficult to see without special stains.
●● Nontuberculous lymphadenitis may show non-necrotizing
granulomas and macrophages with abundant foamy cytoplasm
Fig. 10.5. Granulomatous inflammation due to atypical mycobacteria

(Diff-Quik stain, high magnification; inset: AFB stain, high magnifica-
tion). Numerous epithelioid histiocytes are seen along with the negative
image of several long, beaded mycobacterial organisms seen on DQ stain,
and highlighted with an AFB stain (inset).
because they contain numerous organisms. Mycobacteria-laden

macrophages seen on the Pap stain have been referred to as
pseudo-Gaucher cells. These mycobacteria are more numerous and
this may be seen as a negative image on the Diff-Quik stain and
readily highlighted with acid-fast stains. Some of these myco-
bacteria have distinct morphology. Mycobacterium kansasii
resembles a shepherd’s crook or candy cane and Mycobacterium
fortuitum closely resembles Nocardia spp.
●● Mycobacterial lymphadenitis may also present as acute suppu-
rative lymphadenitis without typical granulomas.
●● Bacillus Calmette-Guérin (BCG) vaccine associated lymphad-
enitis
●● Granulomatous inflammation due to other infections (e.g., cat
scratch disease, fungi)
●● Noninfectious causes of granulomatous inflammation (Table 10.2)

●● Necrotizing lymphadenitis unrelated to infection (e.g., infarction)
●● Foamy histiocytes within lymph nodes can occur with other
infections (e.g., lepromatous leprosy, Whipple disease) and
metabolic storage diseases (e.g., Gaucher disease)
Ancillary Studies
●● Special AFB stains for mycobacteria (Ziehl-Neelsen or Kinyoun
stains)
●● Fluorescence microscopy with fluorochrome dyes such as
auramine O or auramine-rhodamine are more sensitive and spe-
cific than AFB stains
●● Autofluorescence
●● PCR for diagnosis and subclassification
●● Culture for diagnosis and subclassification, although mycobac-
teria are slow growing and culture can take weeks (6–8 weeks
with conventional Lowenstein-Jensen medium and 3 weeks with
Middlebrook liquid and solid media)
Fungal Lymphadenitis
●● Lymphadenitis can result from a variety of fungal infections.
The most common causative agents include Histoplasma capsu-
latum, Coccidioides immitis, and Cryptococcus neoformans.
●● Rare causes of fungal infection like Pneumocystis lymphad-
enitis usually arise in the setting of underlying HIV infection
(Fig. 10.6).
●● Granulomatous or acute inflammation with a necrotic or inflam-
matory background is likely to be encountered. Fungal elements
can be present in varying numbers.
●● C. neoformans has encapsulated yeast forms measuring 5–15 mm.
Their thick capsule causes a clear halo with a DQ stain. The finding
of narrow based budding (tear-drop shape yeast) is very helpful.
●● H. capsulatum is a much smaller round to oval yeast form meas-
uring 2–4 mm. Abundant macrophages in these cases are usually
Fig. 10.6. Fungal lymphadenitis due to Cryptococcus neoformans (H&E

stain, high magnification). Clear (unstained) yeast formation with a thick
halo (capsule) are shown caught up among granulomatous inflammation
in this lymph node FNA. The inset shows encapsulated cryptococcal yeast
(Mucicarmine stain).
laden with intracytoplasmic yeast. One may also find narrow-

based budding.
●● C. immitis has larger thick-walled spherules (cysts) that measure
20–150 mm. When intact they contain 3–5 mm endospores.
Endospores may also be dispersed on the slide if the spherules
are ruptured.
●● Nonfungal granulomatous lymphadenitis (e.g., tuberculosis)
●● Blastomycosis, morphologically similar to Cryptococcus, is an

uncommon cause of lymphadenitis; these organisms are larger,
lack a capsule, and have broad-based budding
Ancillary Studies
●● Histochemical stains for fungi include Grocott or Gomori meth-
enamine silver (GMS) and PAS.
●● Cryptococcus capsule also stains positive with mucicarmine and
Alcian blue stains.
●● A Fontana-Masson stain can be helpful to identify capsule-deficient
Cryptococcus.
●● Specific immunostains may be required if available (e.g.,
Pneumocystis).
●● Fungal culture.
Toxoplasma Lymphadenitis
●● Lymph node infection with the protozoan Toxoplasma gondii
can be congenital (fetal toxoplasmosis) or acquired.
●● Acquired infection causes localized lymphadenopathy, pre-
senting mainly in the posterior cervical nodes, in normal
hosts.
●● Infections usually remain latent and only cause tissue damage
and/or systemic disease in immunocompromised patients.
●● Cytology specimens characteristically show a polymorphous
lymphoid population, epithelioid cell clusters (epithelioid
microgranulomas), and aggregates of monocytoid B-cells with
or without a necrotic background.
●● Cysts with many bradyzoites (“bag of parasites”) and free extra-
cellular tachyzoites of T. gondii are rarely found in aspirates, but
have been reported.
●● Viral lymphadenitis
●● Granulomatous lymphadenitis
Table 10.3. Differential diagnosis

of monocytoid B-cell hyperplasia.
Early cat scratch disease
Toxoplasma lymphadenitis
EBV-related lymphadenopathy
CMV-related lymphadenopathy
Early HIV-related lymphadenopathy
Marginal zone lymphoma
●● Leishmania lymphadenitis
●● Brucella infection (undulant fever)
●● Other causes of increased monocytoid B-cells (Table 10.3)
Ancillary Studies
●● Wright-Giemsa stain for parasites
●● Specific immunocytochemical stain if available
●● PCR using primers designed for the ribosomal DNA of T. gondii
●● Serology (high titers of IgG- and IgM-specific antibodies to
T. gondii is usually necessary for the diagnosis; IgM is usually
positive within 3 months of infection)
Leishmania Lymphadenitis
●● This is an uncommon cause of lymphadenopathy caused by
infection with the protozoan Leishmania, which is transmitted
by sandflies.
●● Infection may be associated with localized nodal infection drain-
ing a focus of cutaneous infection, or with visceral disease and
widespread lymphadenopathy (kala-azar) (Fig. 10.7).
●● Lymph node aspirates contain a polymorphous lymphoid back-
ground, necrotizing or non-necrotizing granulomatous inflam-
mation, and several plasma cells. Necrosis may be suppurative.
●● Organisms may be detected by finding amastigotes within macro-
phages (Leishman-Donovan bodies), or free on the slide follow-
ing rupture of cells, in routinely stained specimens. Amastigotes
are round to oval in shape and range in size from 1 to 3 mm.
Fig. 10.7. Leishmania lymphadenitis (Diff-Quik stain, high magnification).

Several bullet-shaped extracellular amastigotes can be seen scattered
among lymphocytes and histiocytes.
The nucleus and bar-shaped kinetoplast (paranucleus) may not

be visible in all organisms.
●● Leishman-Donovan bodies are more commonly found in cases
with more acute inflammation, and less often in cases with
granulomas or numerous plasma cells.
●● Granulomatous lymphadenitis.
●● Histoplasma lymphadenitis: yeast forms that mimic amastigotes
can be distinguished using a GMS stain which will not stain
Leishmania organisms.
Ancillary Studies
●● Parasites stain with Giemsa stains, but are negative with PAS
and silver stains (GMS)
●● Immunostain if available
●● Serology
●● Culture in appropriate media
●● Animal inoculation
Herpes Simplex Virus Lymphadenitis

●● Lymph node infection and enlargement due to infection by
Herpes simplex virus (HSV) is rare, but has been reported in
inguinal lymph nodes, particularly in patients with hematologi-
cal malignancies.
●● HSV infection manifests as a necrotizing lymphadenitis in
lymph nodes.
●● Cytology samples have abundant necrotic debris with scattered
neutrophils and a mixed lymphoplasmacytic infiltrate, but lack
granulomas.
●● Characteristic HSV viral inclusions such as multinucleation,
margination of chromatin, and molding have been reported to
occur in stromal cells, but not lymphoid cells.
●● Cat scratch disease without granulomatous inflammation
●● Other viral lymphadenitides (e.g., Epstein-Barr virus [EBV], measles)
●● Lymph node infarction
●● Malignancy, particularly hematologic malignancy given that
most patients will have a history of a hematologic malignancy
Ancillary Studies
●● Immunohistochemical or in situ hybridization stain for HSV1/2
(“cocktail”)
●● Viral culture
●● Molecular methods to prove whether infection is due to HSV1
or HSV2
Fig. 10.8. Infectious mononucleosis (Diff-Quik stain, high magnifica-

tion). This FNA is from a lymph node in an 8-year old boy with positive
EBV serology. The lymphoid cells in this aspirate are polymorphous and
include a prominent immunoblastic population and plasmacytoid cells.
Flow cytometry confirmed the absence of a monoclonal population.
Infectious Mononucleosis Lymphadenitis

(EBV Related Lymphadenopathy)
●● Young children and toddlers typically have an asymptomatic
self-limiting infection with EBV, whereas teenagers may have
a more serious and contagious illness presenting with fatigue,
fever, pharyngitis, lymphadenopathy, splenomegaly and some-
times hepatomegaly.
●● Patients classically have tender cervical lymphadenopathy with
a lymphocytosis containing atypical lymphocytes (Downey
cells) reported in their peripheral blood smear (Fig. 10.8).
●● In a lymph node FNA a prominent immunoblast population is
seen within a polymorphous lymphoid background admixed with
tingible body macrophages and plasmacytoid lymphocytes.
●● Occasionally, more pleomorphic atypical immunoblasts with

binucleation, mimicking Reed-Sternberg (RS) cells, will be
seen. Mitoses may be encountered in these cells.
●● The key features that help to distinguish this reactive lymphad-
enopathy from non-Hodgkin lymphoma are the range (polymor-
phous appearance) of lymphoid cells present and the absence of
clonality.
●● Viral lymphadenitis with an infectious mononucleosis-like syn-
drome (HIV, Cytomegaloviral [CMV], HSV, HHV6)
●● Toxoplasma lymphadenitis
●● Autoimmune disease (SLE, rheumatoid arthritis)
●● Lymphadenitis associated with drugs (e.g., phenytoin)
●● Vaccination associated lymphadenitis
●● Non-Hodgkin lymphoma
●● Hodgkin lymphoma
Ancillary Studies
●● Heterophil antibody testing (Paul-Bunnell test), MonoSpot test
(more sensitive assay), and EBV-specific serology studies can
be performed when infection is clinically suspected. The incu-
bation of the virus is 40–60 days, so serology is usually positive
at presentation.
●● Immunostains: Unlike classical Hodgkin lymphoma, the RS-
like cells in cases of infectious mononucleosis are positive for
pan-B cell markers (CD20) and negative for CD15 and CD30.
●● Flow cytometry should be performed particularly in those
cases with an exuberant immunoblastic reaction that mimics
a non-Hodgkin lymphoma (lymphocytes in reactive EBV
lymphadenopathy are polyclonal). Flow cytometry will not
exclude a Hodgkin lymphoma.
Cytomegaloviral (CMV) Lymphadenitis

●● CMV is a rare cause of lymph node enlargement, which
may present as an asymptomatic infection or with an infectious
mononucleosis-like illness. CMV lymphadenitis can occur at any
age and in immunocompetent or immunosuppressed patients.
●● Involved lymph nodes usually have both reactive follicular

and paracortical hyperplasia. The cells infected by CMV are
histiocytes and occasionally endothelial cells, rather than lym-
phocytes.
●● Polymorphous lymphocytes, as seen in reactive lymphoid hyper-
plasia, are seen with an increase of monocytoid B-cells.
●● Infected cells are often sparse and have characteristic CMV
intranuclear inclusions and sometimes multiple small cytoplas-
mic inclusions.
●● Reactive lymphoid hyperplasia
●● Conditions with monocytoid B-cell hyperplasia (Table 10.3)
●● Toxoplasma lymphadenitis
●● Lymphoma: In classical Hodgkin lymphoma there is membra-
nous CD15 staining, as opposed to cytoplasmic immunoreactiv-
ity seen in CMV infected cells.
Ancillary Studies
●● Immunostains, including CMV immunostains. Cells containing
CMV inclusions express CD15, with a Golgi reaction or diffuse
cytoplasmic pattern.
HIV-Associated Lymphadenopathy
●● Lymph node enlargement occurring in a patient with HIV infec-
tion may be due to HIV infection itself and/or secondary to
co-infection (e.g., tuberculosis), an inflammatory process (e.g.,
Castleman disease or immune reconstitution inflammatory
syndrome), or malignancy (e.g., lymphoma, Kaposi sarcoma,
metastases).
●● An infectious mononucleosis-like syndrome may occur in acute
HIV infection that manifests with lymphadenopathy, pharyngitis,
a rash, and malaise. Chronic HIV-related lymphadenopathy
(progressive generalized lymphadenopathy) tends to present
with generalized lymphadenopathy, with nodes typically under

1 cm in size.
●● Lymph node architecture changes with HIV infection chronicity
and declining immunodeficiency (diminishing CD4 cell count).
Nodal architecture progresses from hyperplastic geographic
reactive follicles (pattern A), to follicle regression (pattern B),
and ultimately presents with a “burnt out” fibrotic lymph node
(pattern C). Late phase (pattern C) lymphadenopathy today is
uncommon as individuals may be on highly active antiretroviral
therapy (HAART).
●● The formation of multinucleated giant cells may be seen in lym-
phoid tissue from HIV positive patients. These cells are pro-
duced by the syncytial aggregate of HIV-infected CD4 cells.
●● The architectural patterns of HIV lymphadenitis may not be
easy to recognize by FNA alone. Patterns A (early HIV infec-
tion) and B (chronic HIV infection) will both show the cyto-
morphologic findings of reactive lymphoid hyperplasia, usually
with admixed plasma cells and monocytoid B-cells. Lymphocyte
depletion with follicular dendritic cells is seen in late stage HIV
lymphadenopathy.
●● Polykaryocytes or giant cells resembling Warthin-Finkeldey
giant cells with hyperchromatic overlapping nuclei and scant
cytoplasm may rarely be seen.
●● Reactive lymphoid hyperplasia
●● Castleman disease
●● Lymphoma
Ancillary Studies
●● HIV status and peripheral blood CD4 cell count
●● p24 immunostain can be performed, with positive staining best
localized to dendritic cells
●● Special stains for mycobacteria and fungal infection as coexist-
ent pathology should always be excluded
Spleen Infections
Bacilliary Peliosis
●● This is a vascular proliferation caused by infection with
B. henselae, occurring mainly in immunocompromised or AIDS
patients.
●● The spleen is rarely affected. More common sites of disease
include the skin (bacillary angiomatosis), lymph nodes, bone,
and liver.
●● Vascular proliferation resembling granulation tissue associated
with both neutrophils and mononuclear inflammatory cells is
the morphologic hallmark.
●● Cytology samples show blood vessels with plump endothelial
cells present in a background of neutrophils, debris, and granu-
lar material.
●● Granular material containing bacteria may be seen.
●● Carrion’s Disease (Oroya fever) caused by Bartonella bacilliformis
●● Granulation tissue
●● Kaposi sarcoma
●● Castleman disease
●● Vascular tumors like hemangioma, littoral cell angioma, and
angiosarcoma
Ancillary Studies
●● Special stains: Gram stain can be used to demonstrate Gram-
negative bacilli. A Warthin-Starry stain will highlight clusters
of the Gram-negative bacilli
●● Immunostain for Bartonella if available
●● Electron microscopy in difficult cases
●● Serology
●● Culture of aspirated material
●● Blood culture
Spleen Infections 253
Splenitis and Splenic Abscess

●● Acute splenitis (also known as acute splenic tumor or septic
spleen) is the result of a massive neutrophilic infiltrate and con-
gestion within the red pulp accompanied by splenomegaly. This
condition may be associated with sepsis or typhoid fever.
●● Splenic abscess contains pus in a walled off area of the spleen. This
usually occurs in the setting of bacterial endocarditis, immunosup-
pression, intravenous drug use, or splenic trauma. Bacteria like Sta-
phylococcus or Streptococcus are the most common pathogens.
●● Aspirates contain abundant neutrophils that may be associated
with inflammatory debris.
●● Bacteria may be identified.
●● Blood contamination with neutrophilia.
Ancillary Studies
●● Gram stain
●● Tissue culture
Mycobacterial Infection
●● Patients infected with mycobacteria can present with diffuse
splenomegaly (e.g., multiple granulomas in miliary tuberculo-
sis) or focal lesions in the spleen (e.g., solid spindle cell nodule
in HIV+ patients).
●● Aspirates procured from granulomas show granulomatous
inflammation with or without necrosis.
●● In cases with atypical mycobacterial infection (e.g., MAI),
specimens usually contain numerous histiocytes with foamy or
granular cytoplasm.
●● FNA of a solid spindle cell nodule will exhibit a predominant

spindle cell population with abundant cytoplasm.
●● Mycobacteria may be seen as a negative image with Diff-Quik
stain.
●● Noninfectious granulomatous disease (e.g., sarcoidosis, chronic
granulomatous disease)
●● Peliosis
●● Felty syndrome (rheumatoid arthritis) where there is expansion
of red pulp cords and sinuses with macrophages
●● Proliferation of foamy macrophages due to other causes such as
ingestion of exogenous mineral oil, immune thrombocytopenic
purpura, metabolic storage disorders (Gaucher disease, Niemann-
Pick disease, Tay-Sachs disease), thalassemia, and hyperlipidemia
●● For splenic spindle cell lesion the differential includes inflam-
matory myofibroblastic tumor, vascular neoplasms like littoral
cell angioma, and sarcoma.
Ancillary Studies
●● Special stains for mycobacteria will be positive for organisms,
which are usually abundant in cases of MAI. In spindle cell nod-
ules the spindle cells contain mycobacteria.
●● Immunostains to characterize spindle cells and exclude a vascu-
lar or other spindle cell tumor. These histiocytic spindle cells are
positive for macrophage markers (e.g., CD68) and negative for
keratin, actin, S-100, ALK, and endothelial antibodies.
●● Tissue culture
Infectious Mononucleosis
●● Splenomegaly in infectious mononucleosis due to EBV infec-
tion may lead to splenic rupture and death.
●● EBV infection results in white pulp hyperplasia without promi-
nent germinal centers, and expansion of the red pulp sinusoids
by immunoblasts.
●● EBV infection may also be associated with hemophagocytic
syndrome in the spleen.
Spleen Infections 255
●● Cytology material will show increased immunoblasts which
have prominent nucleoli.
●● Hemophagocytosis may be evident.
●● Hodgkin and non-Hodgkin lymphoma
●● Hemophagocytic syndrome due to other etiologies
Ancillary Studies
●● Serology for evidence of EBV infection
●● Immunostains such as EBV latent membrane protein (LMP) for
staining EBV infected cells, and lymphoid cell markers to illus-
trate a reactive lymphoid process
●● EBV in situ hybridization (EBER)
●● Flow cytometry to exclude leukemia/lymphoma
Hydatid Cyst
●● Hydatid cysts due to Echinococcus granulosus infection (cystic
echinococcosis) can rarely occur in the spleen.
●● FNA of the cyst wall will show scattered fragments of an
acellular, laminated membrane.
●● Aspiration of fluid (hydatid sand) may yield numerous invagi-
nated protoscoleces that bear hooklets as well as individual
scattered hooklets (18–35 mm in length). Hooklets are usually
present for longer because they resist degeneration.
●● Noninfectious splenic cysts (epithelial, mesothelial)
●● Pseudocyst
●● Lymphangioma
Ancillary Studies
●● Serology to confirm exposure to the parasite.
Suggested Reading
Caponetti G, Pantanowitz L. HIV-associated lymphadenopathy. Ear Nose
Throat J. 2008;87:374–5.
Gaffey MJ, Ben-Ezra JM, Weiss LM. Herpes simplex lymphadenitis. Am
J Clin Pathol. 1991;95:709–14.
Gupta SK, Kumar B, Kaur S. Aspiration cytology of lymph nodes in
leprosy. Int J Lepr Other Mycobact Dis. 1981;49:9–15.
Hadfield TL, Lamy Y, Wear DJ. Demonstration of Chlamydia trachomatis
in inguinal lymphadenitis of lymphogranuloma venereum: a light
microscopy, electron microscopy and polymerase chain reaction study.
Mod Pathol. 1995;8:924–9.
Monaco SE, Schuchert MJ, Khalbuss WE. Diagnostic difficulties and pit-
falls in rapid on-site evaluation of endobronchial ultrasound guided fine
needle aspiration. Cytojournal. 2010;7:9.
Shimizu K, Ito I, Sasaki H, Takada E, Sunagawa M, Masawa N. Fine-needle
aspiration of Toxoplasmic lymphadenitis in an intramammary lymph
node: a case report. Acta Cytol. 2001;45:259–62.
Silverman JF. Fine needle aspiration cytology of cat scratch disease. Acta
Cytol. 1985;29:542–7.
Solis OG, Belmonte AH, Ramaswamy G, Tchertkoff V. Pseudogaucher cells
in Mycobacterium avium intracellulare infections in acquired immune
deficiency syndrome (AIDS). Am J Clin Pathol. 1986;85:233–5.
Stanley MW, Steeper TA, Horwitz CA, Burton LG, Strickler JG, Borken S.
Fine-needle aspiration of lymph nodes in patients with acute infectious
mononucleosis. Diagn Cytopathol. 1990;6:323–9.
Tallada N, Raventós A, Martinez S, Compañó C, Almirante B. Leishma-
nia lymphadenitis diagnosed by fine-needle aspiration biopsy. Diagn
Cytopathol. 1993;9:673–6.
11
Breast, Skin,
and Musculoskeletal Infections
Pam Michelow1, Walid E. Khalbuss2,
1
University of the Witwatersrand and National Health Laboratory Service,
2
A plethora of infections may involve the skin, soft tissue, and

musculoskeletal system. Almost all of these infections are ame-
nable to being diagnosed by cytology using scrapings, split-skin
smears, and fine needle aspiration. This chapter covers the cytopa-
thology of infectious diseases in the breast, skin, subcutaneous
tissue, deep soft tissue, bone and joints.
Breast Infections
●● Breast cytology including FNA and infrequently nipple dis-
charge evaluation may be useful in the management of breast
infections.
●● Most inflammatory lesions of the breast are benign in nature
(Table 11.1).
●● The most common microrganisms are bacteria, especially Sta-
phylococcus aureus, including methicillin-resistant Staphyloco-
ccus aureus (MRSA).
●● Unusual pathogens reported to involve the breast include cat
scratch disease, mycobacteria (tuberculosis and atypical myco-
bacteria), actinomycosis, fungi (e.g., Cryptococcus, Aspergillus,

258 11. Breast, Skin, and Musculoskeletal Infections
Table 11.1. Inflammatory lesions of the breast.

Infectious
Acute mastitis
Puerperal mastitis
Breast abscess
Subareolar abscess
Mycobacterial infection
Fungal infections
Cat scratch disease
Actinomycosis
Herpes simplex virus
Parasitic infections
Typhoid mastitis
Myiasis (maggot infestation)
Benign inflammatory (noninfectious)
Duct ectasia (periductal mastitis)
Granulomatous lobular mastitis (idiopathic)
Plasma cell mastitis
Fat necrosis
Silicone mastitis
Diabetic mastopathy
Sarcoidosis
Vasculitis
Phlebitis (Mondor disease)
Breast infarct
Collagen vascular disease
Amyloid tumor
Mastitis factitia (self-inflicted mastitis)
Malignant inflammatory (noninfectious)
Inflammatory breast carcinoma
dimorphic fungi, chromomycosis), parasites, and maggot infes-

tation. A rare case with herpes simplex virus cells has been
reported in a hemorrhagic nipple discharge.
●● Chronic infections may mimic breast cancer clinically, on imag-
ing studies, and microscopically. They may manifest as a breast
mass, with calcifications, inflammatory skin changes, and axil-
lary lymphadenopathy.
●● Unusual infections have been reported to be the initial presenta-
tion of HIV infection.
●● Foreign bodies (e.g., nipple piercing, breast implants) occasion-
ally result in associated infection.
Breast Infections 259
●● Breast cancer, particularly malignancies causing skin ulceration,

can become secondarily infected. In such cases, it is important
that malignant cells are not overlooked when there is an associ-
ated intense inflammatory background.
●● Lymphoma (e.g., marginal zone lymphoma) of the breast should
not be mistaken for chronic inflammation, nor should myeloid
sarcoma be mistaken for acute inflammation.
Acute Mastitis and Abscess

●● Mastitis is defined as inflammation of the breast with/without
infection. Mastitis with infection may be lactational (puerperal)
or nonlactational (e.g., related to mammary duct ectasia).
●● A breast abscess is a localized area of infection with a walled-off
collection of pus. Breast abscess develops in 5–10% of women
with mastitis. Approximately 50% of infants with neonatal mas-
titis will develop a breast abscess. Aspiration of purulent mate-
rial should always be submitted for culture.
●● Subareolar abscess (Zuska disease) is an abscess located in the
periareolar area of the breast, associated with squamous meta-
plasia of the lactiferous ducts, keratin plugging, duct dilation,
and rupture. The exact etiology is unknown, but there may be an
infective component.
●● Mastitis due to infection is usually caused by bacteria. Most
infections are due to S. aureus, followed by coagulase-negative
staphylococci.
●● Many cases, particularly abscesses, may be polymicrobial due
to aerobes and anaerobes (Fig. 11.1).
Clinical Features
●● Acute breast infections typically affects women 15–45 years of
age (especially those lactating), infants under 2 months of age,
and adolescent girls. Breast infection in men is rare, and may
signify an underlying immune deficiency.
●● Patients usually present with a tender breast mass. They may also
have a purulent nipple discharge, drainage of pus from a mam-
mary fistula, and tender ipsilateral axillary lymphadenopathy.
●● Atypical presentations include bilateral breast mastitis and/or
breast abscesses, multiple breast abscesses, nipple inversion
and/or retraction, and septicemia and/or toxic shock syndrome.
Fig. 11.1. Acute mastitis. (Top left) Numerous neutrophils are shown from
a breast aspirate consistent with a breast abscess (Pap stain, high magnifi-
cation). (Bottom left) A group of reactive ductal epithelial cells is present
in a background of neutrophils from a case of acute mastitis (Diff-Quik
stain, high magnification). (Right) Anucleated squamous cells are shown
in a background of acute inflammation obtained from a subareolar abscess
caused by duct ectasia (top image is a Pap stain of intermediate magnifica-
tion; bottom image is a Diff-Quik stain at higher magnification).
●● Numerous neutrophils are the hallmark of an acute infection.
Frank pus may be obtained on aspiration.
●● Background necrosis and admixed inflammatory cells (eosi-
nophils, lymphocytes, plasma cells, and histiocytes) may be
noted.
●● Occasionally the causative pathogen or foreign material may be
noted.
●● Reactive ductal epithelial cells may be observed including cell
enlargement and prominent nucleoli. These cells are cohesive
and have associated myoepithelial cells compared with duct
carcinoma.
Breast Infections 261
●● The presence of numerous anucleate and nucleated squamous

cells with keratin debris associated with inflammatory cells,
including foreign-body type giant cells, is indicative of duct
ectasia.
Ancillary Studies
●● Special stains (e.g., Gram stain, acid-fast stain)
Chronic and Granulomatous Mastitis

●● Chronic granulomatous inflammation of the breast may be
related to infection (e.g., mycobacteria, fungi), a noninfectious
etiology (e.g., sarcoidosis, Wegener’s granulomatosis, foreign
material including leakage from silicone implants), or an idio-
pathic condition (referred to as granulomatous lobular mastitis).
●● Tuberculous (TB) mastitis is rare, even in tuberculosis-endemic
countries, with a reported incidence of under 3%.
●● Idiopathic granulomatous mastitis is an exceedingly rare breast
condition.
Clinical Features
●● Chronic breast infections may mimic breast cancer.
●● TB mastitis can present as a painless mass (nodular, diffuse, or
sclerosing type), breast edema, tender abscess, or with draining
sinuses.
●● The hallmark feature is the finding of epithelioid macrophages
lying singly or present in clusters.
●● Varying quantities of multinucleated giant cells, lymphocytes,
plasma cells, neutrophils, necrosis and ductal epithelial cells,
with or without reactive atypia, may be seen.
●● Rarely the causative agent (e.g., fungal elements) may be seen.
Ancillary Studies
●● Polarization for foreign material
●● Special stains (Gram, Ziehl-Neelsen, PAS and/or GMS)
●● Microbiology culture including mycobacterial and fungal

cultures
●● Immunocytochemistry (e.g., CD68 for macrophages)
●● Molecular studies (e.g., PCR for mycobacteria)
Parasitic Breast Infections

●● Parasite infections typically present as a hard breast mass, and
sometimes as an abscess. Persistent infections with old worms
and/or embedded ova may present as calcifications on mam-
mography.
●● Mammary filariasis seen in tropical regions (India, China, South
America) is mainly caused by Wuchereria bancrofti. FNA can
detect microfilariae and adult worms. Eosinophils in these aspi-
rates are a common finding.
●● Other parasitic infections reported to occur in the breast include
schistosomiasis, mammary cysticercosis, hydatid cyst, sparag-
nosis, and Trichinella infections.
Skin and Soft Tissue Infections

●● Skin infections can be diagnosed by Tzanck preparations, slit-
skin smears, and FNA of palpable lesions, vesicles, and/or cysts
(Figs. 11.2–11.6).
Tzanck preparation. Scrapings taken from a vesicle or pustule
(ideally taken from the base of the lesion) may show herpes
simplex and varicella zoster cytopathic effect. In addition, the
waxy cytoplasmic inclusions (molluscum bodies) of Mollus-
cum contagiosum can be seen (Fig. 11.2).
Slit-skin smear. These smears are to be performed by making
an incision involving an active lesion approximately 5 mm

long and 3 mm deep. Pinching the skin decreases bleeding.
The tissue is then scraped and slides prepared looking for
microorganisms such as Mycobacterium leprae in leprosy or
leishmaniasis.
●● A wide variety of infections may involve the skin and under-
lying soft tissue (Table 11.2). Deep soft tissue infections that
may be encountered include cellulitis, abscesses, necrotizing
Skin and Soft Tissue Infections 263
Fig. 11.2. Molluscum contagiosum. (Top left) An AIDS patient is shown

with widely disseminated molluscum skin lesions. Some of the papules
have a dimple in their center. (Bottom left) Skin biopsy shows keratinoc-
ytes containing large intracytoplasmic inclusions compressing the nucleus
to the edge of the cell forming so-called molluscum bodies (H&E stain,
intermediate magnification). (Right) Molluscum bodies are shown in a
cytology sample present among inflammatory cells (top image with Pap
stain and lower image with MGG stain, both at high magnification) (the
right images are courtesy of Dr. Pawel Schubert, University of Stellen-
bosch, Cape Town, South Africa).
fasciitis, gangrene (e.g., Clostridial gas gangrene), cryptococ-

coma (Fig. 11.3), protothecosis and pyomyositis (suppurative
myositis).
●● Skin abscesses are mostly due to Staphylococcus spp., but many
bacteria including Streptococci spp., Clostridium spp., and
actinmycoses can cause them. Purulent material comprised of
numerous neutrophils is noted.
●● Granulomatous inflammation can be attributed to infections
(e.g., mycobacteria) or noninfectious causes (e.g., sarcoidosis,
foreign body reaction to a ruptured epidermal inclusion cyst).
Fig. 11.3. Cryptococcosis. (Left) The images shown are from an HIV
positive patient that presented with a large neck mass (cryptococcoma)
suspected to be an extranodal soft tissue lymphoma based on radiologi-
cal studies. There was no cervical lymphadenopathy seen. The specimen
shows granulomatous inflammation associated with extra- and intracel-
lular fungal organisms surrounded by a clear halo due to the cryptococcal
capsules (Diff-Quik stain, high magnification). (Right) Histopathologic
image showing yeasts in macrophages and giant cells (H&E stain, high
magnification).
●● Tuberculosis of the skin is traditionally classified into (1) pri-

mary infection, (2) secondary disease or reinfection (which
includes lupus vulgaris, tuberculosis verrucosa, scrofuloderma,
orificial, and disseminated cutaneous tuberculosis), and (3) cuta-
neous reactions (tuberculids) to a distant tuberculous infection.
Scrofuloderma is involvement of the skin due to direct extension
from underlying lymphadenitis, usually due to atypical myco-
bacteria. Atypical mycobacteria may also result in uncommon
infections such as Buruli ulcer (Mycobacterium ulcerans) and
swimming pool granuloma (Mycobacterium marinum). Myco-
bacterial specimens usually show granulomatous inflammation
with/without necrosis associated with acid-fast bacilli.
Fig. 11.4. Leprosy. (Left) A large foamy multinucleated macrophage is

shown with vacuoles of various sizes (lepra cell) in an inflamed back-
ground (Pap stain, high magnification). (Right) Numerous bacteria can be
seen within a lepra cell (Fite stain, high magnification) (images courtesy
of Dr. Pawel Schubert, Stellenbosch University, Cape Town).
●● Occasionally cytology samples may contain arthropods and

related structures. Follicle mites (Demodex), measuring approx-
imately 0.4 mm in length, are often located around the face,
upper neck, and chest. Demodex folliculorum is found within
hair follicles and Demodex brevis in sebaceous glands. These
mites may cause folliculitis and possibly perifollicular inflam-
mation (demodicosis). Cytologic findings in skin scrapings
include mites that may be associated with squamous epithelial
cells, and in cases of Demodex folliculitis with acute inflamma-
tion and hair follicle components. Mites still attached to hairs
may be seen. They need to be differentiated from scabies (Sar-
coptes scabei) which can also measure up to 0.4 mm in length.
Jellyfish nematocysts (cylindrical hyaline structures) have been
reported in skin scrapings. Myiasis is an infestation of the skin
Fig. 11.5. Dermatophytosis. FNA in this case was obtained from multiple
purulent neck masses caused by infection due to Trichophyton violaceum.
(Left) Pink staining fungal elements are shown at high magnification with
a Pap stain that can also be appreciated as negative images on the Diff-
Quik stain (top right). Branching fungal hyphae are readily visible with a
methenamine silver stain (bottom right, high magnification) (images cour-
tesy of Dr. Pawel Schubert, Stellenbosch University, Cape Town).
by developing larvae (maggots) of a variety of fly species (e.g.,

botfly and tumbu fly). The diagnosis in cytologic material has
been reported.
Leprosy
●● Leprosy is a slowly progressive infection due to M. leprae. This
organism is an intracellular Gram-positive bacterium that is also
acid-fast, although less so than Mycobacterium tuberculosis.
●● Cytology has been utilized in the diagnosis and classification
of leprosy, as well as the evaluation of bacteriologic (bacterial
index [BI]) and morphologic indices (MI) (Fig. 11.4).
Fig. 11.6. Dematiaceous fungi. (Left) Portion of a wood splinter is shown

among inflammatory cells in this cell block identified in an elbow subcu-
taneous mass FNA (H&E stain, intermediate magnification). (Top right) A
multinucleated giant cell is shown containing several round stacked brown
(naturally pigmented) sclerotic bodies. These vegetative fungal cells
resemble “copper pennies.” Note the marked background inflammatory
debris (H&E stain, high magnification). (Bottom right) Polymorphous
hyphae with odd intercalated swellings are shown in a granulomatous
background of this phaeomycotic cyst (PAS stain, high magnification).
Clinical Features
●● Leprosy involves mainly the skin, nasal mucosa, and peripheral
nerves.
●● There are five different categories depending on the host
response (Ridley-Jopling scale). These include tuberculous,
borderline tuberculoid, mid-borderline, and borderline leproma-
tous and lepromatous leprosy.
●● The WHO recommends classifying leprosy according to the
number of lesions and presence of bacilli on a skin smear. The
Table 11.2. Spectrum of skin infections.

Viral
Poxviridae (e.g., molluscum contagiosum)
Herpesviridae (e.g., HSV, varicella, Kaposi sarcoma)
Papoviridae (e.g., verruca vulgaris, warts, condyloma acuminatum)
Other viral diseases (e.g., HIV, HTLV-1)
Bacterial
Superficial pyogenic infections (e.g., impetigo, ecthyma)
Deep pyogenic infections (e.g., cellulitis, erysipelas, necrotizing fasciitis)
Corynebacterial infections (e.g., erythrasma, trichomycosis)
Neisserial infections
Mycobacterial infections (tuberculosis, atypical mycobacteria, leprosy)
Miscellaneous infections (e.g., cat scratch disease, chancroid, tularemia)
Bacillary angiomatosis
Spirochetal
Treponematoses (syphilis, bejel, yaws, pinta)
Borrelioses
Mycoses
Superficial filamentous infections (dermatophytoses, dermatomycoses)
Yeast infections (e.g., candidasis, cryptococcosis)
Systemic mycoses (e.g., blastomycoses, histoplasmosis, zygomycoses)
Dematiaceous fungi (chromomycosis, phaeohyphomycosis, sporotrichosis)
Hyalohyphomycoses
Mycetoma
Botryomycosis
Parasitic
Protozoal (e.g., acanthamebiasis, leishmaniasis, toxoplasmosis)
Helminths (e.g., cysticercosis, onchocerciasis, dirofilariasis)
Algal
Protothecosis
Infestations and animal injuries
Arthropods (e.g., demodex, scabies, pediculosis, myiasis)
Miscellaneous (e.g., marine injuries from jellyfish)
two categories are paucibacillary leprosy (five or less lesions

with an absence of organisms on smear) and multibacillary
leprosy (six or more lesions with possible visualization of bacilli
on smear).
●● The organism cannot be grown in vitro, and requires animal
inoculation in mice or armadillos.
●● The cytomorphology of lepromatous and borderline leproma-
tous leprosy include large numbers of neutrophils and foamy
macrophages (lepra cells).
●● Lepra cells may be multinucleated with round to oval nuclei,
finely granular chromatin, and inconspicuous nucleoli. The cells
have abundant cytoplasm containing vacuoles of various sizes.
Necrosis associated with a fatty background and epithelioid
histiocytes may be seen.
●● In tuberculoid and borderline tuberculoid leprosy, noncaseating
granulomas comprised of epithelioid histiocytes, Langhans-type
giant cells, and lymphocytes are seen.
●● Negative images of mycobacteria may be encountered on
Romanowsky-stained slides.
●● With acid-fast stains, the bacilli are visible both intra- and
extracellularly, 3–7 mm in length and may be beaded, straight,
or curved.
●● Bacilli are readily found in lepromatous and borderline lesions,
but are scanty in borderline tuberculoid and not usually found in
tuberculoid leprosy.
●● Acid-fast stained smears can be used to determine a BI and
Morphological Index (MI). The BI is an index of the bacillary
load in the patient (density of bacteria is based on counting AFB
per high power fields). The MI is an index of bacilli viability.
Solid bacilli are judged to be viable while fragmented or granu-
lar bacilli are interpreted to be nonviable. At least 200 discrete
bacilli should be evaluated.
●● Other granulomatous infections (e.g., leishmaniasis, toxoplas-
mosis, histoplasmosis, mycobacteria)
●● Noninfectious granulomatous reactions (e.g., foreign body)
●● Sarcoidosis
●● Sinus histiocytosis
●● Whipple’s disease
●● Lipid granuloma
●● Histiocytic disorders (e.g., Gauchers and Niemann-pick disease)
Ancillary Studies
●● Special stains (e.g., Fite)
●● Immunocytochemisry (M. lepra PGL-1 antibody test)
●● Molecular studies (PCR)
●● Lepromin skin test and lymphocyte transformation test (both usu-
ally positive in tuberculoid and borderline tuberculoid leprosy)
Cutaneous Mycoses
●● A large proportion of infectious skin diseases are caused by fungi.
These include dermatophytoses (ringworm), yeasts (e.g., Candida,
Cryptococcus, dimorphic fungi), and the dematiaceous fungi.
●● Dermatophytosis is a common fungal infection of the skin (tinea),
hair (e.g., kerion), and nails (onychomycosis). The many kerati-
nophilic fungal species belong to the genera Microsporum, Tricho-
phyton, and Epidermophyton. Infections are generally made using
skin scrapings examined microscopically with 10% potassium
hydroxide, by biopsy or culture. Deep infections (pseudomyc-
etoma) are uncommon, but when they occur these fungi cause a
mixed suppurative and granulomatous reaction (Fig. 11.5).
●● Sporotrichosis is caused by infection with the dimorphic fungus
Sporothrix schenckii, usually following percutaneous implan
tation from infected vegetable matter (e.g., splinter, rose thorn).
A single nodule at the trauma site may develop and subse-
quently spread as multiple nodules along local lymphatics.
These nodules can ulcerate. Visceral involvement may rarely
occur in immunosuppressed patients. Specimens demonstrate
granulomas with or without abscesses and sometimes the pres-
ence of PAS positive hyaline material due to increased immune
deposits. Sporothrix organisms may appear as yeast-like forms
(2–8 mm), elongated cells (so-called cigar bodies) that measure
2–4 × 4–10 mm, or rarely true hyphae. These fungal elements
stain with PAS, GMS, and anti-Sporothrix antibodies. They
need to be differentiated from the septate hyphae and spores of
alternariosis caused by Alternaria spp.
●● Dematiaceous (pigmented) fungi are divided into two clinico-
pathological groups (Fig. 11.6):
Chromomycosis (chromoblastomycosis). This chronic fungal
infection mainly affects the legs. It is caused by many fungi

(Fonsecaea pedrosi, Phialophora carrionii, Aureobasidium

pullulans, Rhinocladiella aquaspersa). Lesions are charac-
terized by granulomas with or without suppuration. Fungal
forms are round, thick walled, golden brown due to their pig-
ment, septate cells (called sclerotic bodies, muriform cells,
or medlar bodies) that measure 5–12 mm. They may be free
or within giant cells. PAS and GMS stains may obscure their
natural pigment leading to a misdiagnosis.
Phaeohyphomycosis (phaeochromomycosis) includes a
heterogeneous group of superficial, subcutaneous, and vis-
ceral infections. Common organisms include Exophiala
spp., Wangiella dermatidis, Curvularia pallescens, Phoma
spp., Cladophialophora bantiana, Cladosporium spp., and
Phialophora richardsiae. Patients with systemic infections
are usually immunosuppressed. Infection usually results in
the formation of a circumscribed cyst or abscess, associated
with granulomatous inflammation. Foreign material like a
wood splinter is often found together with brown filamentous
hyphae and yeast-like structures in a background of inflam-
matory debris.
●● Mycetoma is a chronic infection of the skin and subcutaneous
tissue that presents with draining sinuses that discharge colored
(black, red, yellow, or pale) grains (aggregates of organisms).
These lesions can extend deep into underlying bone. There
are two etiologic types: actinomycetic mycetoma (caused by
Actinomycetes or Nocardia spp.) and eumycotic (maduromy-
cotic) mycetomas (caused by true fungi).
●● Botryomycosis (bacterial pseudomycosis) is a chronic bacterial
infection of the skin associated with suppuration and sinuses
that drain small white granules composed of causal bacteria
(e.g., S. aureus).
Cutaneous Parasites
●● Parasitic infections that may involve the skin include ameba, flag-
ellates (e.g., trypanosomes, leishmaniasis), trematodes (e.g., schis-
tosomiasis), cestodes (e.g., cysticercosis, echinococcocis), and
nematodes (e.g., onchocerciasis, dirofilariasis, larva migrans).
●● Leishmaniasis. Infection due to Leishmania may manifest with
cutaneous (oriental), mucocutaneous (American) and visceral
(kala-azar) disease (see also Chap. 4). Cutaneous (“dry” and

“wet”) leishmaniasis is a self-limited granulomatous condition
of the skin with acute, chronic, recidivous (lupoid) and dissemi-
nated forms. Acute lesions contain massive amounts of chronic
inflammatory cells, including parasitized macrophages. Chronic
skin lesions contain fewer infected macrophages. A CD68 stain
may help accentuate parasitophorous vacuoles containing organ-
isms. Parasites may rarely be found in spindled fibroblasts. The
parasites (amastigote phase) are round to oval and contain an
eccentrically located kinetoplast. The kinetoplast may be lost
with hydropic degeneration (swelling) of parasites, which is
often the case when there is an associated marked acute inflam-
matory reaction. These organisms (Leishman-Donovan bodies)
are best seen with a Giemsa stain. PCR can be used to confirm
the diagnosis, even on old or dried material.
●● Cysticercosis. Human cysticercosis caused by infection with
the larval stage of Taenia solium (pork tapeworm) commonly
manifests as subcutaneous and intramuscular nodules. Common
sites of involvement include brain, muscle, eye, and heart. The
larvae also have a predilection for subcutaneous tissue of the
trunk, thighs, and upper arms. Nodular lesions, that may clini-
cally resemble a lipoma or neurofibroma, are amenable to FNA.
The nodules are composed of a cyst (usually 1 cm) filled with
clear or milky white fluid and an ovoid larva (called a cysticer-
cus cellulosae) that measures 3–10 × 4–5 mm attached at one
end. The scolex has a rostellum, four suckers, and 22–32 hook-
lets in two rows. The cyst (bladder) wall is multilayered (100–
200 mm thick), may be encased in fibrotic tissue and associated
with eosinophils, chronic inflammatory cells, and foreign body
giant cells. Cysticerci only cause an inflammatory response
when they degenerate, not when they are viable. A cytological
diagnosis can be easily made in cases where the actual parasite
structure (scolex of the cysticercus larva) is identified in smears.
However, in cases where the only finding is inflammatory cells
(eosinophils, histiocytes) or granulomas present in a dirty gran-
ular background, these features should alert the pathologist to
this possibility. When the cytological diagnosis of a parasitic
cyst is suggested an excision biopsy should be recommended.
Positive serology may be helpful.
Bone and Joint Infections 273
Bone and Joint Infections

●● Osteomyelitis may be caused by infection (viral, bacterial, myco-
bacterial, and fungal including mycetoma) and noninfectious
causes (e.g., acute fracture, sarcoidosis, histiocytic proliferation).
●● Bacterial osteomyelitis may result from hematogenous spread
(typically when bacteria are implicated), contiguous spread (e.g.,
diabetic foot, chronic leg ulcers) or direct inoculation (e.g., open
fracture, introduction of orthopedic hardware). Bacterial osteo-
myelitis is most often due to S. aureus infection, typically acute,
occurs mainly in the long bones of children, and elicits a suppu-
rative inflammatory response that includes osteonecrosis. Osteo-
myelitis of the jaw may involve Actinomyces. Bacteria that may
cause a granulomatous reaction include Salmonella, Brucella,
Bartonella, Coxiella burnetii (causes Q fever), and Burkholde-
ria pseudomallei (causes melioidosis) (Fig. 11.7).
●● Mycobacterial osteomyelitis may be due to M. tuberculosis,
atypical mycobacteria and leprosy. Tuberculous bone infections
may be localized (e.g., Pott’s disease of the spine). However,
immunosuppressed patients such as those with AIDS frequently
have multifocal bone involvement. Typically these specimens
show necrotizing granulomatous inflammation.
●● Fungal osteomyelitis may be attributed to almost all fungi. Bone
involvement may occur from an isolated multisystem infection.
Fungi that commonly demonstrate hematogenous spread to bone
are Candida spp., Cryptococcus, and most of the dimorphic
fungi. Radiology images may indicate significant bone destruc-
tion, often with accompanying soft tissue infection.
●● Parasitic osteomyelitis is mainly due to infection with Echinoc-
occus (hydatid disease).
●● Arthritis may be caused by infection of the joints (septic arthri-
tis). Bacteria are the most common cause of synovial infec-
tion, including septic bursitis. Typical bacterial culprits include
Staphylococcus, Streptococci, Gonococcus, Meningococcus,
polymicrobial infections including anerobes, Lyme disease, and
mycobacteria. A wide variety of viral infections (e.g., Parvovi-
rus B19, Hepatitis B and C, HIV, Alphavirus) can lead to joint
inflammation (rheumatic syndrome). Although less common,
fungal causes of arthritis may be due to Candida, Cryptococcus,
Fig. 11.7. Acute osteomyelitis. (Left) FNA of bone showing acute inflam-
matory cells and debris that included groups of bacterial cocci (upper left
inset) (Diff-Quik stain, high magnification). (Right) The images shown
are from a 49-year-old female who presented with a thoracic vertebral
lesion radiologically significant for osteomyelitis. (Top right) Most of the
specimen shows marked cellular debris and acute inflammatory cells (Pap
stain, high magnification). (Bottom right) The cell block in this latter case
shows similar marked acute inflammation associated with osteonecrotic
bone fragments (H&E stain, high magnification). A Gram stain on cell
block material was positive for Gram-positive cocci.
Aspergillus, dimorphic fungi, and nearby mycetoma. Infection

will need to be differentiated from noninfectious causes such as
acute rheumatic fever and poststreptococcal arthritis. Synovial
fluid characteristics as well as culture results may be helpful in
this regard (Table 11.3).
Bacillary Angiomatosis
●● Bacillary angiomatosis is an unusual vascular proliferation
caused by infection with Bartonella henselae.
●● It is seen predominantly in patients with AIDS, and may resemble
Kaposi sarcoma clinically. However, cases in immunocompetent
Table 11.3. Synovial fluid characteristics in septic arthritis.
Condition Appearance Color Consistency Cellularity Other elements
Normal Clear Yellow Viscous No or rare (<25%) neutrophils No clots, crystals or organisms
Viral Cloudy Yellow Low viscosity Lymphocytes and some neutrophils (>50%) May clot
Bacterial Cloudy Gray-green Low viscosity Abundant neutrophils (>75%) Often clots, culture positive
Fungal Variable Variable Low viscosity Lymphocytes and some neutrophils (>50%) None
Crystals Cloudy White Low viscosity Many neutrophils (<90%) Crystals
Bone and Joint Infections
275
persons and after organ transplantation have been described. If

not treated, it may be life-threatening.
●● Bone and soft tissue lesions may present with or without accom-
panying skin lesions. Skin lesions resemble pyogenic-like gran-
ulomatous inflammation.
●● Histologically, lesions are characterized by a lobular prolifera-
tion of blood vessels lined by plump endothelial cells with an
epithelioid appearance. The vessels are surrounded by a dense,
neutrophilic infiltrate, and clusters of bacilli that can be high-
lighted with a Warthin-Starry silver stain.
●● The cytologic features are largely nonspecific including a speci-
men that contains blood and acute inflammatory cells.
●● The diagnosis is best made on cell block material and with ancil-
lary studies. The cell block will show a proliferation of small
blood vessels, including some that are ectatic and filled with
fibrin, erythrocytes, neutrophils, and leukocytoclastic debris.
●● Blood vessels are lined by plump endothelial cells protruding into
the vascular lumen. These endothelial cells have round or oval
nuclei with moderate atypia, vesicular chromatin, and nuclear
membrane folding. Their cytoplasm is finely vacuolated.
Ancillary Studies
●● Special stain (the organisms can be detected with a Warthin-
Starry silver stain).
●● Immuncytochemistry (Bartonella antibodies are now available).
●● Electron microscopy (these studies will show an extracellular
aggregation of bacilli that have trilaminar walls including two
electron-dense layers separated by a less electron-dense layer).
Suggested Reading
Dabiri S, Hayes MM, Meymandi SS, Basiri M, Soleimani F, Mousavi MR.
Cytologic features of “dry-type” cutaneous leishmaniasis. Diagn
Cytopathol. 1998;19:182–5.
EL Hag IA, Fahal AH, Gasim ET. Fine needle aspiration cytology of
mycetoma. Acta Cytol. 1996;40:461–4.
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Gupta RK, Naran S, Lallu S, Fauck R. Cytologic diagnosis of molluscum

contagiosum in scrape samples from facial lesions. Diagn Cytopathol.
2003;29:84.
Handa U, Garg S, Mohan H, Garg SK. Role of fine-needle aspiration
cytology in tuberculosis of bone. Diagn Cytopathol. 2010;38:1–4.
Kapila K, Verma K. Diagnosis of parasites in fine needle breast aspirates.
Acta Cytol. 1996;40:653–6.
Malik A, Bhatia A, Singh N, Bhattacharya SN, Arora VK. Fine needle aspi-
ration cytology of reactions in leprosy. Acta Cytol. 1999;43:771–6.
Nemenqani D, Yaqoob N, Hafiz M. Fine needle aspiration cytology of
granulomatous mastitis with special emphasis on microbiologic cor-
relation. Acta Cytol. 2009;53:667–71.
Rao RN, Krishnani N, Malhotra K, Suresh B, Mehrotra R. Dilemmas in
cytodiagnosis of subcutaneous swellings: mimics and look-alikes of
cysticercosis. J Clin Pathol. 2010;63:926–9.
Silverman J, Lannin D, Unverferth M, Norris H. Fine needle aspira-
tion cytology of subareolar abscess of the breast. Spectrum of cyto-
morphologic findings and potential diagnostic pitfalls. Acta Cytol.
1986;30:413–9.
Thompson KS, Donzelli J, Jensen J, Pachucki C, Eng AM, Reyes CV.
Breast and cutaneous mycobacteriosis: diagnosis by fine-needle aspira-
tion biopsy. Diagn Cytopathol. 1997;17:45–9.
hgbjkdfg
12
Head and Neck Infections
Pam Michelow1, Walid E. Khalbuss2,
1
2
Many patients present with lesions of the head and neck. These
may be congenital, infectious, cystic, reactive, inflammatory, or
neoplastic in nature. Clinical examination and radiologic imaging
may not be sufficient to render an accurate diagnosis. Cytologic
evaluation in the form of smears and fine needle aspiration (FNA)
in this anatomical region is a rapid and accurate diagnostic modality
with good sensitivity and specificity for infectious diseases. This
chapter covers several key infections likely to be encountered in
this site. Infections involving cervical lymph nodes are addressed
in Chap. 10.
Salivary Gland Infections

●● Bacteria, viruses, and fungi may all cause acute or chronic
sialadenitis.
●● The most common bacterium associated with infection of the
salivary glands is Staphylococcus aureus. Other bacteria include
Hemophilus influenza, Klebsiella pneumonia, Salmonella spp.,
Pseudomonas aeruginosa, Prevotella, and Porphyromonas
spp., Fusobacterium, Peptostreptococcus spp., mycobacterium,
cat scratch bacillus, Treponema pallidum, actinomyces, and
Burkholderia pseudomallei (melioidosis).

280 12. Head and Neck Infections
●● The most common cause of viral parotitis is paramyxovirus

(mumps). Other viruses including influenza, parainfluenza,
Coxsackie viruses A and B, ECHO virus, and cytomegalovirus
have been cultured from salivary fluid in acute sialadenitis.
●● Fungal infections of the salivary gland, mainly Candida and
Cryptococcus have been reported.
●● Rare parasitic infections described in the salivary glands include
toxoplasmosis, cysticercosis, Enterobius, and hydatid disease.
Acute Sialadenitis
●● Acute infection can involve any salivary gland, but is more
common in the major glands (especially the parotid).
●● Factors that increase the risk of infection are salivary stasis,
salivary duct stenosis, dehydration, diabetes mellitus, anorexia,
bulimia, hypothyroidism, malnutrition, HIV/AIDS, Sjögren’s
syndrome, and certain medications.
●● Acute sialadenitis may result in an abscess. Patients present with ten-
der, indurated, enlarged, ill-defined swelling of their salivary glands.
Pus may discharge via the salivary duct orifice into the oral cavity.
●● A neutrophilic infiltrate may be associated with destruction of duc-
tal epithelium and loss of acini, especially with abscess formation
(Fig. 12.1).
●● A marked inflammatory infiltrate that consists mainly of neu-
trophils with associated fibrin and debris is common.
●● Occasional duct cells, sometimes with marked reactive changes,
can be noted. Reactive atypia may mimic a neoplasm. Restricted
numbers and limited atypia of epithelial cells in the presence of
acute inflammation suggest sialadenitis rather than a neoplasm.
●● Stone fragments may be seen if there is an associated sialo-
lithiasis.
●● Nontyrosine (amylase type) crystalloids (5–200 mm) may be iden-
tified. They are nonbirefringent, geometric in shape (rectangular,
rhomboid), and typically fragment in aspirated material. They
stain orange with Pap stain and pink in H&E stained cell blocks.
●● Granulation tissue may be present.
Salivary Gland Infections 281
Fig. 12.1. Acute sialadenitis. (Top left) Direct smear of a fine needle
aspiration (FNA) from a parotid gland showing numerous neutrophils and
debris consistent with acute sialadenitis. Culture revealed Staphylococcus
aureus (Pap stain, intermediate magnification). (Bottom left) Gram stain
from a salivary gland FNA showing scattered Gram-positive bacteria
(high magnification). (Right) Nontyrosine crystalloids admixed with acute
inflammatory cells in a case of acute sialadenitis (H&E stain, cell block,
Ancillary Studies
●● Special stains (Gram stain, silver stain)
Chronic Sialadenitis
●● Chronic sialadenitis due to infection may present as a distinct
mass, usually in the parotid gland. Noninfectious causes (e.g.,
Küttner’s tumor) can have similar changes (Table 12.1).
●● Chronic inflammation causes loss of acini, fibrosis, and duct
dilatation.
Table 12.1. Differential diagnosis of chronic sialadenitis.

Condition Cytomorphology Comment
Reactive lymphaden- Polymorphous lymphocytes Within or adjacent to
opathy glands
Tingible body macrophages Contaminating epithe-
Lymphohistiocytic aggregates lium can be present
Benign lymphoepithe- Polymorphous lymphocytes History of HIV or
lial cyst Epithelial cells Sjögren syndrome
Proteinaceous background
Diffuse lymphocytosis Increased CD8+ lymphocytes History of HIV
syndrome
Wharthin tumor Polymorphous lymphocytes Resembles oncocytic
Oncocytes metaplasia
Cystic background
Branchial cleft cyst Benign squamous cells Located outside salivary
Reactive lymphocytes gland
Granular debris
Mucoepidermoid Malignant cells (mucinous Cellular aspirate
carcinoma and/or squamous)
Background debris
Possible mucin
Non-Hodgkin Monomorphic (atypical) Ancillary studies
lymphoma lymphocytes required
●● Salivary epithelial cells are scant, especially acinar cells which
are reduced in both size and number. Ductal cells may undergo
squamous, mucinous, goblet, or oncocytic metaplasia.
●● The background may contain blood, mucus, debris, varying
numbers of mononuclear inflammatory cells, and fibrous tissue
fragments.
●● Microorganisms are rarely identified.
Ancillary Studies
●● Special stains (e.g., Gram, GMS, PAS, acid-fast stains)
●● Serology (for Sjögren’s syndrome)
●● Immunophenotyping (e.g., flow cytometry) to exclude a non-
Hodgkin lymphoma
Thyroid Gland Infections 283
Granulomatous Sialadenitis
●● There are infectious and several noninfectious causes (e.g.,
sarcoidosis, Wegener’s granulomatosis).
●● Infections include mycobacteria, histoplasmosis, toxoplasmo-
sis, cat scratch disease, and rhinosporidiosis. Infection of the
salivary gland may be the primary site of presentation.
●● Patients usually present with a firm, unilateral, or bilateral
swelling with or without pain. Occasional cases may produce
draining sinuses and facial nerve palsy, mimicking cancer.
●● Epithelioid and possible multinucleated histiocytes are present
with a variable background of acute and chronic inflammatory
cells with/without necrosis.
●● Inflammation with foamy macrophages and associated reactive
epithelial atypia can be mistaken for mucoepidermoid carcinoma.
●● The causative organism (e.g., mycobacteria, fungi) may be seen.
Ancillary Studies
●● Special stains for mycobacteria (AFB) and fungi (GMS, PAS)
●● Immunocytochemistry (macrophages are CD68 positive)
●● Serology (e.g., toxoplasmosis, autoimmune disease)
●● PCR for microorganisms
Thyroid Gland Infections

●● Infective thyroiditis is an infrequent occurrence (Table 12.2).
This is because the thyroid gland is relatively resistant to infec-
tion due largely to iodine concentration. Cultures may reveal a
single agent or polymicrobial infection (approximately 30% of
cases).
●● In children, infection usually occurs when the thyroid is joined
directly to the oropharynx (e.g., congenital pyriform sinus fistula).
Thus, the causative agents are those that spread contiguously
from the oral cavity to the thyroid.
Table 12.2 Causes of infective thyroiditis.

Viral
Measles, influenza, EBV, CMV, enterovirus, adenovirus, echovirus, mumps,
St. Louis encephalitis viruses
Bacterial
(Common) Streptococcus, Staphylococcus, Peptostreptococcus spp.,
Gram-negative bacilli
(Uncommon) Klebsiella spp., Haemophilus influenza, Salmonella spp., Entero-
bacteriaceae, Eikenella corrodens, mycobacteria, actinomycosis, Bartonella,
Treponema pallidum
Fungal
Coccidiomycosis, Aspergillosis, Cryptococcosis, Histoplasmosis, Candidiasis,
Pneumocystis jirovecii
Parasitic
Hydatid disease, Strongyloides stercoralis, cysticercosis, malaria
●● In adults, infection may be from hematogenous spread, a

thyroglossal duct remnant, underlying neoplasia (e.g., infected
fistula), or direct extension from a nearby site (e.g., esophagus,
neck abscess). Patients with immunosuppression (e.g., HIV
positive) are at increased risk.
●● There have been occasional case reports where FNA resulted in
the development of acute suppurative thyroiditis, emphasizing
the need to maintain sterility when performing an FNA.
●● The presentation may be acute or insidious with a painful, swollen
thyroid. Dysphagia, dystonia, fever, and erythema of the skin
overlying the thyroid may be noted. De Quervain thyroiditis
clinically may mimic acute thyroiditis. Thyroid function tests
are usually normal.
●● Bacteria tend to cause acute suppurative thyroiditis (acute
inflammatory cells), whereas viral infections present mainly
with subacute thyroiditis.
●● On FNA, a marked inflammatory infiltrate with numerous
neutrophils, macrophages, and debris is seen. Follicular cells,
with or without reactive atypia, may be encountered. Occasion-
ally the causative organism is noted.
●● The presence of associated fluid and/or foamy macrophages with
follicular cells favors the diagnosis of an infected thyroid cyst.
●● In the absence of native thyroid epithelium, it may not be possible
to distinguish acute thyroiditis from an abscess in a lymph node.
Radiologic imaging may help determine the site.
Oropharyngeal Infections 285
●● In anaplastic carcinoma, scant malignant cells may be masked

by an intense inflammatory infiltrate. If the patient does not
respond to antimicrobial agents, an alternative diagnosis should
be considered.
●● The causative organism may not always be seen in cytologic
material. Therefore material should be stained (Gram, AFB,
GMS, PAS) and aspirates submitted for microbiology culture
(aerobic and anerobic bacteria, mycobacteria, fungi).
●● Granulomatous (De Quervain) thyroiditis often presents with a
tender thyroid that mimics acute thyroiditis clinically. Multinu-
cleated giant cells are a prominent feature in addition to granulo-
matous inflammation and occasional degenerated follicular cells.
●● Autoimmune (Hashimoto’s thyroiditis) presents with a dif-
fusely enlarged thyroid that, on occasion, may be painful. FNA
yields a heterogeneous population of lymphocytes, plasma
cells, macrophages, and lymphohistiocytic aggregates in addi-
tion to Hürthle cells.
Oropharyngeal Infections
●● Normal oropharyngeal flora do not usually cause disease.
Altered local factors, systemic disease, and unusual organisms
may overcome the defensive mechanism of this flora to cause
infection.
●● Many viral infections can involve the oropharynx such as herpes
viruses, HIV, HPV, EBV, rubeola (measles), rubella, mumps,
and Molluscum contagiosum.
●● HPV transmission can be sexual or vertical. The latter route
of infection may be related to juvenile onset laryngeal papil-
lomatosis. Oral verruca are due to HPV 2 and 4, focal epithelial
hyperplasia due to HPV 13, benign condyloma and papilloma-
tosis due to HPV 6 and 11, and squamous cell carcinoma related
to HPV types 16, 18, 31, 33, and 35. HPV related lesions in
this location do not exfoliate easily and their diagnosis is based
primarily on histology, not cytology.
●● Peritonsillar abscess (quinsy) is the most common deep infection
in the head and neck. FNA will show abscess material. It is usually
the result of a polymicrobial infection.
●● Although a wide variety of fungal infections may affect the

oral mucosa, candidiasis is the most common yeast infection of
the oropharynx.
●● Parasites that involve the oropharynx include cysticercosis (tape-
worm), echinococcosis (hydatid disease), trichinosis (round worm),
and mucocutaneous leishmaniasis (also known as espundia).

●● Herpes simplex virus (HSV) is a DNA virus. HSV-1 is trans-
mitted through infected saliva or active perioral lesions while
HSV-2 is spread by sexual contact. Both types may cause oral
lesions. Clinical lesions associated with both types are indistin-
guishable.
●● Primary HSV oral lesions occur predominantly in small children
and are associated with fever, malaise, and neck lymphadenopathy.
Painful oral lesions may extend from the mouth to the lips,
coalesce, and ulcerate.
●● Latent infection residing in ganglia may re-activate (e.g., following
stress or immunosuppression) causing a secondary herpetic lesion
(cold sore or fever blister), often on the lips.
●● A Tzanck preparation or smear (vesicle-based scraping submitted
for microscopic examination) is often done to diagnose HSV
infection (Fig. 12.2).
●● Herpetic viral changes of Cowdry type A and B are evident,
which includes nuclear enlargement and molding, multinucleation,
peripheral condensation of chromatin, and eosinophilic intranu-
clear inclusions.
●● Acute and chronic inflammatory cells and debris are seen in the
background.
●● The cytomorphology resembles varicella zoster virus infection,
but the clinical picture differs.
Ancillary Studies
●● Immunocytochemistry for HSV
●● Direct fluorescent assay
Fig. 12.2. Oral herpes simplex virus (HSV) infection showing charac-
teristic viral cytopathic changes with (left image) Pap stain, (top right)
Diff-Quik stain, and (bottom right) in H&E stained cell block material
●● PCR for viral DNA

●● Serology
●● Viral isolation from tissue culture
Cervicofacial Actinomycosis
●● Actinomyces are filamentous, branching, Gram-positive anaerobic
bacteria. The most common isolate is Actinomyces israelii.
Almost all species are commensals of the mouth.
●● Cervicofacial infection often involves the jaw (“lumpy jaw”)
leading to multiple abscesses, extensive fibrosis, and sinuses from
which pus with sulfur granules (bacterial colonies) may drain.
●● Trauma (like tooth extraction) or immunosuppression, are pre-
disposing factors for actinomycosis (Figs. 12.3 and 12.4).
Fig. 12.3. Oral actinomyces flora. (Left image) Filamentous bacteria are
shown without associated acute inflammatory cells (Pap stain, high mag-
nification). Actinomyces granules without inflammation are shown in this
tonsillectomy specimen, which are frequently embedded within tonsillar
crypts (H&E stain, intermediate magnification).
●● Cytologic specimens contain long, thin, and sometimes branched
filamentous bacteria that may radiate from a central area within
a sulfur granule.
●● True infection is usually associated with numerous neutrophils,
unlike contamination from oral flora.
Ancillary Studies
●● Special stains (e.g., Gram, Ziehl-Neelsen, Fite). Actinomy-
ces needs to be distinguished from Nocardia as actinomyces
responds to penicillin while Nocardia is treated with sulfa drugs.
Unlike actinomyces, Nocardia often stains with acid-fast stains.
Actinomyces also tends to stain well with GMS.
Fig. 12.4. Actinomycosis. This image shows a cluster of Actinomyces

filamentous bacteria surrounded by acute inflammatory cells in an FNA
obtained from an infected cervical lymph node in an HIV positive patient
(Pap stain, high magnification) (image courtesy of Dr. Pawel Schubert,
Stellenbosch University, South Africa).
Oral Candidiasis
●● Candida normally colonizes the oral cavity. Clinical evidence of
infection (candidiasis or candidosis) depends on the immune sta-
tus of the host, mucosal environment, and strain of Candida spp.
●● Candida albicans is most frequently associated with oral can-
didiasis.
●● Clinical presentations include pseudomembranous candidiasis
(thrush), central papillary atrophy, cheilitis, as well as erythema-
tous, hyperplastic, and mucocutaneous lesions.
●● Oral Candida may be the presenting feature of HIV infection or
other cause of immunosuppression (Fig. 12.5).
Fig. 12.5. Oral candidiasis. (Left image) Oral smear showing abundant
pseudohyphae and yeasts of Candida albicans (PAS stain, intermediate
magnification) (photo courtesy of Dr. Shabnum Meer, University of the
Witwatersrand, South Africa). (Right image) Many spores can be seen
associated with debris in this case where Candida contaminated a herpetic
oral ulcer (Diff-Quik stain, high magnification).
●● Pseudohyphae and/or yeasts are seen. Pseudohyphae are elon-
gated and constricted along their length. Yeasts are round to oval
in shape and 2–4 mm in size.
●● Candida glabrata exists only in a yeast form, with no pseudo-
hyphae.
●● If yeasts are prominent, the differential includes histoplasmosis,
cryptococcosis, and blastomycosis.
●● If pseudohyphae predominate, they need to be distinguished
from Aspergillus (septate and branches at 45°) and mucromy-
cosis (aseptate and branches at 90°), both of which do not form
budding yeasts.
Sinonasal Infections 291
●● Reactive squamous epithelial and inflammatory cells are present

in the background.
●● There may be associated bacteria and pathology related to
another underlying entity (e.g., herpes, carcinoma).
Ancillary Studies
●● Wet mount (saline and 10% potassium hydroxide) prepared
from fresh material.
●● Special stains (PAS with diastase, GMS, others). Candida is
also Gram positive.
Sinonasal Infections
●● Infections of the nasal cavity and sinuses are common.
●● Typical viral infections are due to rhinovirus, adenovirus, parain-
fluenza, and influenza viruses.
●● Staphylococcus aureus, Streptococci spp., Peptostreptococci
spp., and Pseudomonas aeruginosa are common bacteria asso-
ciated with sinusitis. Bacterial rhinosinusitis, however, is an
uncommon complication of acute viral rhinosinusitis.
●● Sinonasal fungal infections may be:
Noninvasive. This includes a fungal ball (also called myce-
toma or if appropriate, aspergilloma), allergic fungal rhinosi-

nusitis, and saprophytic infection. Nasal discharge cytology
has been used to diagnose allergic fungal sinusitis, looking
for fungal hyphae of Aspergillus, as well as thick allergic-
type mucin, eosinophils, and Charcot-Leyden crystals.
Invasive. Such mycotic infections may be due to mucormycosis
(zygomycosis), aspergillosis, and Fusarium. Mucormycosis

is most commonly due to infection with the class Zygomyc-
etes (e.g., Mucor, Rhizopus, Absidia spp.). The ribbon-like
fungal hyphae of such zygomycetes are nonseptate or pau-
ciseptate, branch at right angles, and usually associated with
necrosis (Fig. 12.6).
●● Several infectious diseases of the nose and paranasal sinuses
can present with granulomatous inflammation. These include
not only invasive fungal rhinosinusitis, but also rhinoscleroma,
Fig. 12.6. Mucormycosis (phycomycosis). The image shows broad

nonseptate hyphae within fibrinopurulent material identified in a 70-year
male patient with fungal sinusitis (H&E stain, high magnification). Cul-
ture grew out Rhizomucor spp. in this case (image courtesy of Dr. Raja
Seethala, University of Pittsburgh Medical Center, USA).
rhinosporidiosis, tuberculosis, and leprosy. The differential

diagnosis also includes noninfectious causes like sarcoidosis
and Wegner’s granulomatosis.
●● Parasites such as fly larvae may be identified in the nasal cavity.
Rhinoscleroma
●● Rhinoscleroma (or just scleroma) is associated with the bacterium
(coccobacillus) Klebsiella rhinoscleromatis, acquired by direct
inhalation of infected material.
●● Specimens show a mixed inflammatory infiltrate of plasma
cells, lymphocytes, and foamy macrophages (called Mikulicz
cells) that contain bacteria.
●● Bacteria stain with silver stains like the Warthin-Starry stain.
Infected Embryologic Cysts 293
Rhinosporidiosis
●● Rhinosporidiosis is due to chronic infection with Rhinosporidium
seeberi, believed to be an aquatic protistan parasite rather than a
fungus. Contact with stagnant water is a risk factor. This infec-
tion is endemic in India and Sri Lanka.
●● In addition to infecting the upper airways (causing polypoid
mucosal lesions), the conjunctiva and skin may be involved.
●● Specimens show sporangia and endospores present in a back-
ground of mixed inflammatory cells (plasma cells, lymphocytes,
histiocytes, neutrophils, and possible giant cells) and metaplas-
tic columnar cells. Neutrophils tend to form rosettes around the
spores.
●● The sporangia are large (100–300 mm), thick walled, and contain
hundreds to thousands of small round endospores (6–12 mm).
●● Sporangia and spores both stain with PAS, GMS, and muci-
carmine.
●● The differential diagnosis includes Coccidioides immitis, which
produces spherules (30–60 mm), and Mucorales, which pro-
duces sporangia (30–70 mm). Myospherulosis may also mimic
rhinosporidiosis (see Chap. 15).
Infected Embryologic Cysts

●● Embryologic cysts in the head and neck region (e.g., branchial
cleft cyst, thyroglossal duct cyst, cystic hygroma) may become
infected.
●● These cysts are often asymptomatic until they become
infected.
●● Infected cysts on FNA yield purulent material containing numer-
ous neutrophils and debris.
●● Inflamed cysts can show reactive changes that may mimic squa-
mous cell carcinoma.
●● Repeated infections can cause fibrosis and the lining epithe-
lium to become denuded and replaced by granulation tissue
(Figs. 12.7 and 12.8).
Fig. 12.7. FNA of an infected branchial cleft cyst in a 39-year old male
shows abundant neutrophils mixed with benign squamous cells (Pap stain,
low magnification).
Eye Infections
●● All structures of the eye can become infected.
●● Specimens from the eye suitable for cytologic evaluation include
conjunctival and corneal scrapings and aspirates of the anterior
chamber, vitreous cavity, and lacrimal glands.
●● Impression cytology of the ocular surface utilizes a collection
device, usually filter paper, applied to the conjunctiva or cor-
nea and then removed. This provides well-preserved cells and is
suitable for microscopic evaluation as well as PCR, flow cytom-
etry, immunocytochemistry, and culture. HSV, Acanthameba,
varicella-zoster virus, adenovirus, and rabies have been diag-
nosed using impression cytology in combination with various
ancillary techniques.
●● Pththirus pubis (crab louse) may infect eye lashes and could
therefore be present as a contaminant on specimens procured
from the eye.
Eye Infections 295
Fig. 12.8. Infected branchial cleft cyst. The aspirate contains mucinous
and metaplastic epithelium present with acute inflammatory cells (Diff-
Quik stain, left intermediate magnification, middle image high magnifica-
tion). The cell block contains fragments of granulation tissue (H&E stain,
right image, intermediate magnification).
Viral Ophthalmic Infections

●● Viruses can infect the eyelids (e.g., herpes simplex), lacrimal
apparatus (e.g., Epstein Barr virus), conjunctivae (e.g., adeno-
virus), intraocular structures (e.g., cytomegalovirus), and the
cornea (keratitis).
●● Herpes simplex keratitis is one of the most important causes
of viral keratitis and is associated with significant morbidity
and mortality. Viral inclusions are rarely identified with cor-
neal scraping and ancillary investigations such as PCR, ISH,
and electron microscopy may be required. Immunoreactivity
for HSV in these samples may be predominantly present in the
cytoplasm rather than the nucleus.
Chlamydial Eye Infection

●● Trachoma, caused by Chlamydia trachomatis, is an important
cause of blindness. Infection may lead to inversion of the upper
eyelids, misdirected eyelashes, corneal scarring, and visual loss.
●● Cytologic evaluation of conjunctival scrapings, swabs, and
ocular impression cytology is useful for making the diagnosis,
although diagnostic ancillary studies such as direct fluorescent
antibody tests and culture are being used more frequently.
●● Cytomorphology of Romanowsky-stained smears shows lym-
phocytes, neutrophils, and conjuctival cells with basophilic
intracytoplasmic inclusions.
Bacterial Eye Infection

●● Infection of the lacrimal gland is usually bacterial in nature.
Staphylococcus aureus is the most common pathogen but other
pathogens include streptococci, gonococci, mycobacteria, and
syphilis.
●● Bacterial conjunctivitis usually presents with a purulent
discharge that may be examined microscopically. Infection may
be due to a variety of bacteria such as Neisseria gonorrhea,
Neisseria meningitides, and Staphylococcus.
●● Drying of the cornea or hypoxia predispose to infection with
Staphylococci, Streptococci, and Pseudomonas.
●● Intraocular bacterial infection may be due to surgery, trauma, and
hematogenous spread. The best source of material for microscopic
evaluation and culture is vitreous fluid, in which neutrophils are
present. A Gram stain in such samples is necessary.
Fungal Eye Infection

●● The cornea is by far the most common site of ocular fungal
infection. Trauma is an important predisposing factor as is topi-
cal steroid use.
●● Corneal scrapings are suitable for microscopic evaluation, spe-
cial stains, and culture.
●● Conjuctival specimens may reveal Candida, Sporothrix
schenckii, and Rhinosporidium seeberi.
Eye Infections 297
Fig. 12.9. Ocular cryptococcosis. FNA of the vitreous fluid in this patient
revealed (left image) encapsulated Cryptococcal yeasts (Pap stain, high
magnification) with narrow-based budding (top right image) (H&E stain,
cell block, high magnification). (Bottom right image) Yeasts stain posi-
tively with mucicarmine stain (high magnification).
●● Fungal keratitis is often due to filamentous species (e.g., Fusarium,

Candida, and Aspergillus).
●● In the vitreous, the presence of macrophages and multinucle-
ated giant cells indicates a granulomatous process, suggestive
of mycobacterial infection (Fig. 12.9).
Parasitic Eye Infection

●● Conjunctival scrapings are useful to diagnose fly larvae, nema-
todes, and trematodes.
●● Acanthameba keratitis can occur after trauma to the cornea, and
has been reported following the use of unsterile saline contact
lens solution. Corneal scrapings are examined for characteristic
trophozoites and cysts (round to oval, 12–18 mm, double-walled)
on Romanowsky, calcofluor white, and trichrome stains, in
addition to fluorescent microscopy and culture. The background
contains reactive epithelium.
●● Aspirates from the anterior chamber can be used to diagnose

Entameba histolytica and nematodes. Parasites can be the cause
of neutrophils in vitreous samples.
Ear Infections
●● While otic smears for cytologic evaluation are a useful tech-
nique used in veterinary practice, they are not utilized much in
human medicine.
●● Otitis externa (swimmer’s ear) is caused by excessive moisture
remaining in the ear canal, or disruption of the ear canal mucosa
by trauma.
●● The most common bacteria responsible for outer ear infections
are Staphylococcus aureus and Pseudomonas aeruginosa. Other
bacteria are less common. In a minority of cases (less than 10%),
a fungus is the cause of swimmer’s ear.
●● Confirmation of infection can be achieved by culture, rather
than cytologic examination of smears.
Suggested Reading
Braz-Silva PH, Magalhães MH, Hofman V, Ortega KL, Ilie MI, Odin G,
et al. Usefulness of oral cytopathology in the diagnosis of infectious
diseases. Cytopathology. 2010;21:285–99.
Deshpande AH, Munshi MM. Rhinocerebral mucormycosis diagnosis by
aspiration cytology. Diagn Cytopathol. 2000;23:97–100.
Gori S, Scasso A. Cytologic and differential diagnosis of rhinosporidiosis.
Acta Cytol. 1994;38:361–6.
McQuone S. Acute viral and bacterial infections of the salivary glands.
Otolaryngol Clin North Am. 1999;32:1–17.
Rivasi F, Longanesi L, Casolari C, Croppo GP, Pierini G, Zunarelli E,
et al. Cytologic diagnosis of Acanthamoeba keratitis. Report of a case
with correlative study with indirect immunofluorescence and scanning
electron microscopy. Acta Cytol. 1995;39:821–6.
Sah SP, Mishra A, Rani S, Ramachandran VG. Cervicofacial actino-
mycosis: diagnosis by fine needle aspiration cytology. Acta Cytol.
2001;45:665–7.
Schnadig VJ, Rassekh CH, Gourley WK. Allergic fungal sinusitis. A report
of two cases with diagnosis by intraoperative aspiration cytology. Acta
Cytol. 1999;43:268–72.
13
Immunosuppressed Host
Pam Michelow1, Sara E. Monaco2,
1
2
Immunosuppression is the result of reduced activity or efficiency

of the host immune system to fight infection. An individual may
be immunosuppressed due to a congenital condition (e.g., severe
combined immunodeficiency or SCID), an acquired condition (e.g.,
human immunodeficiency virus [HIV] infection, autoimmune dis-
ease), or an iatrogenic cause (e.g., transplantation, splenectomy,
chemotherapy, or immunosuppression drugs such as corticos-
teroids or cyclosporine). A weakened immune system for other
reasons is said to be immunocompromised. Potential etiologies in
these patients are diverse, including common community-acquired
infections to uncommon opportunistic infections (Fig. 13.1). While
the inflammatory response associated with many microbial infec-
tions in this setting is often impaired, unusual cases may result
in pseudotumor formation following infection simulating malig-
nancy. Moreover, the quantity and morphology of several microor-
ganisms is likely to be altered because of prophylactic therapy and/
or antimicrobial resistance. The risk of infection in such patients is
usually dependent upon their epidemiologic exposure (e.g., latent
infection with reactivation, nosocomial infection), degree of
immunosuppression (e.g., lowered CD4 count in an HIV positive
patient), and comorbid conditions (e.g., indwelling catheter). An
overview of specific infections and conditions in the immunosup-
pressed patient is reviewed in this chapter.

300 13. Immunosuppressed Host
Fig. 13.1. Penicillium marneffei infection in AIDS. This dimorphic

fungus is an opportunistic pathogen which has emerged to become an
AIDS-defining illness in the endemic areas of Southeast Asia. Cytology
specimens used to make the diagnosis include FNA of lymph nodes, spu-
tum cytology, and touch smears of skin. The images show several yeasts
associated with white blood cells in (left) peripheral blood and (right)
marrow (May-Grünwald Giemsa stain, high magnification) (images cour-
tesy of Kit-Fai Wong, Queen Elizabeth Hospital, Hong Kong).
Transplantation
●● Posttransplant infections (Table 13.1) may occur early after
transplantation (first month), after an intermediate period (1–6
months), or after 6 months.
Early period: Infection may be derived from the donor or
recipient (e.g., CMV, Toxoplasma gondii), surgical complica-

tions (line sepsis, aspiration pneumonia), or hospitalization.
Intermediate period: Patients are at greatest risk for devel-
oping an opportunistic infection due to exogenous immu-

nosuppression. This includes Pneumocystis pneumonia,
Transplantation 301
Table 13.1. Transplant-related opportunistic infections.

Viral
Herpes simplex virus (HSV)
Varicella zoster virus (VZV)
Epstein–Barr virus (EBV)
Adenovirus
Merkel cell polyomavirus (MCPyV)
BK polyomavirus
Human papillomavirus (HPV)
Bacterial
Listeria monocytogenes
Nocardia
Legionella
Mycobacterium tuberculosis
Atypical mycobacteria (M. avium intracellulare or MAI)
Fungal
Candida
Aspergillus
Cryptococcus neoformans
Pneumocystis jirovecii
Trichosporon beigelii
Fusarium
Zygomycetes
Histoplasma capsulatum
Coccidioides immitis
Parasitic
Toxoplasma gondii
BK polyomavirus, respiratory viruses, mycobacteria, and

gastrointestinal parasites.

Late period: These transplant recipients are at stable and
often reduced levels of immunosuppression. They are at risk

for developing common infections (e.g., community-acquired
pneumonia) and/or more rare infections (e.g., disseminated
histoplasmosis).
●● In the transplant patient, viral coinfection may cause direct effects
(clinical infection with symptoms such as esophagitis or diarrhea)
and indirect consequences such as oncogenesis (e.g., EBV-related
posttransplant lymphoproliferative disorder or PTLD, human
herpesvirus-8 [HHV8] associated Kaposi sarcoma).
Human Immunodeficiency Virus (HIV) Infection

●● The hallmark of HIV infection is characterized by this retrovi-
rus leading to selective depletion of CD4 T-lymphocytes. This
acquired immune deficiency allows for the development of
opportunistic infections and neoplasia.
●● The stages of HIV infection include (1) primary infection
(so-called acute seroconversion syndrome), (2) seroconver-
sion (development of detectable antibodies), (3) clinical latent
period (with or without persistent generalized lymphadenopa-
thy or PGL), (4) early symptomatic infection (previously called
acquired immunodeficiency syndrome [AIDS]-related complex
or ARC), (5) AIDS, and (6) advanced HIV disease (CD4 count
<50/mm3).
●● Normal CD4+ T-cell blood count measurements are ³500 cells/
mm3. CD4+ below 200 cells/mm3 is indicative of AIDS. Other
conditions that may also define an AIDS diagnosis are shown
in Table 13.2.
●● HIV may induce a direct viral cytopathic effect on host cells,
mainly lymphoid and histiocytic cells, by causing the formation
of multinucleated giant cells. These p24-positive Warthin-
Finkeldey-type giant cells may be observed rarely in lymph
node specimens and in abundance in fine needle aspirates of
salivary gland lymphoepithelial lesions.
●● Mortality and morbidity associated with HIV infection has
declined since the advent of combination antiretroviral therapy
(ART), also called highly active antiretroviral therapy (HAART).
●● Immune reconstitution inflammatory syndrome (IRIS) occurs
in some HIV-infected patients after commencing ART leading
to a paradoxical worsening of symptoms. Microorganisms fre-
quently associated with IRIS include Cryptococcus, mycobacte-
ria, varicella zoster, herpes virus, and cytomegalovirus.
Human Papilloma Virus (HPV)-Related Disease

●● Immunosuppressed individuals are at increased risk of HPV-
associated malignancies including cervical, anal, penile, vulvar,
vaginal, and oropharyngeal carcinoma.
Human Papilloma Virus (HPV)-Related Disease 303
Table 13.2. AIDS-defining conditions.

Infections
Pneumocystis pneumonia
Esophageal and airway candidiasis
Disseminated atypical mycobacterial infection
Tuberculosis
Cytomegalovirus disease (including retinitis)
Recurrent bacterial pneumonia
Toxoplasmosis
Chronic cryptosporidiosis
Disseminated histoplasmosis
Chronic herpes simplex
Progressive multifocal leukoencephalopathy (JC virus)
Chronic intestinal isosporiasis
Chronic intestinal cryptosporidiosis
Extrapulmonary cryptococcosis
Disseminated or extrapulmonary coccidioidomycosis
Neoplasms
Kaposi sarcoma
Large B-cell non-Hodgkin lymphoma
Invasive cervical cancer
Other
Wasting
HIV-associated dementia (and encephalopathy)
Lymphoid interstitial pneumonia (in children under 13 years)
●● While many HPV-related conditions associated with HIV

have decreased with HAART, their incidence has remained
unchanged.
Cervicovaginal Disease
●● HIV-infected women harbor a wider range of HPV types, have
more persistent HPV, higher rates of progressive squamous
intraepithelial lesion (SIL), and present with invasive cervical
cancer 10–15 years earlier than HIV-negative counterparts with
more advanced disease.
●● With HIV infection there is a tenfold increase in the rate of
abnormal Pap tests compared to HIV-negative women, espe-
cially when the CD4 count falls below <200 cells/mm3.
●● Although there are currently no consensus guidelines,

HIV-infected women should undergo more frequent Pap test
screening and/or HPV testing.
Anal Disease
●● Invasive squamous cell carcinoma of the anus, associated with
high-risk HPV types, is higher among HIV-positive women
and men, especially in men who have sex with men (MSM).
The incidence continues to increase despite the widespread use
of ART.
●● Anal cytology (Anal Pap test) is covered in detail in Chap. 7. The
sensitivity of anal cytology to identify anal squamous lesions
ranges between 69 and 93%, but suffers from low reported spe-
cificity (32–59%).
●● There are currently no consensus guidelines regarding anal
screening.
●● Unlike cervical cancer, HPV testing of anal cytology samples
has shown poor positive predictive value for high grade anal
intraepithelial neoplasia (AIN).
Lymphadenopathy
●● HIV-related lymphadenopathy may occur at any stage of HIV
disease and can be due to a wide variety of reactive, infectious,
and neoplastic causes (Table 13.3). Most of these entities are
discussed in detail in Chap. 10.
●● The most common FNA diagnoses made from HIV-related
lymph nodes are reactive lymphadenopathy followed by infec-
tion and then malignancy.
●● Rare infectious causes of HIV lymphadenopathy may be encoun-
tered such as Pneumocystis jirovecii lymphadenitis.
●● HIV-infected patients are at increased risk of developing mul-
ticentric Castleman disease (MCD), which is often associated
with HHV8 infection. Although atypical follicular dendritic
cells are thought to be diagnostic of Castleman disease, they are
not consistently found on FNA of lymph nodes.
Oropharyngeal Disease 305
Table 13.3. Causes of HIV-related lymphadenopathy.

HIV-associated lymphadenopathy
Mycobacterial infection (tuberculous, atypical and BCG-related)
Suppurative lymphadenitis (bacterial infection including mycobacteria)
Fungal infection (e.g. Cryptococcosis, histoplasmosis)
Viral infection (e.g., EBV, CMV, HSV)
Castleman disease
Non-Hodgkin lymphoma
Hodgkin lymphoma
Kaposi sarcoma
Bacillary angiomatosis
Metastatic cancer
●● On occasion, more than one disease may be encountered in the

same lymph node (e.g., mycobacterial infection together with
Kaposi sarcoma or lymphoma) (Fig. 13.2).
Oropharyngeal Disease
●● Immunosuppressed patients, especially those with HIV infec-
tion, may manifest with diverse diseases of the oropharynx.
●● Oral candidiasis. True infection should be suspected when fun-
gal elements (yeasts, hyphae, and pseudohyphae) are intermin-
gled with inflammatory cells and debris. The presence of thrush
is a frequent source of Candida contamination in gastrointesti-
nal and respiratory tract samples (e.g., bronchoalveolar lavage)
in these patients.
●● Oral hairy leukoplakia (OHL) (Fig. 13.3). This EBV-associated
disease causes white patches on the side of the tongue, typically
with a corrugated or hairy appearance, but can also be smooth
and flat. Cytology specimens may show prominent nuclear
beading (peripheral margination and clumping of chromatin),
eosinophilic intranuclear inclusions, and ground glass nuclei.
Detection of EBV DNA can be confirmed by PCR or in situ
hybridization, as well as viral culture.
●● Herpes simplex virus. The diagnosis can be confirmed using a
Tzanck smear, immunohistochemical stains for HSV1/2, direct
fluorescent assay, PCR for viral DNA, and viral culture.
Fig. 13.2. Tuberculous lymphadenitis due to Mycobacterium tubercu-

losis infection. (Left) Lymph node FNA showing classic granulomatous
inflammation morphology with a Langhans type giant cell and adjacent
epithelioid histiocytes (Pap stain, high magnification). (Top right) Myco-
bacterial infection consisting predominantly of necrosis (Pap stain, low
magnification). (Bottom right) Mycobacterial infection presenting as an
abscess with numerous neutrophils in a necrotic background (Pap stain,
intermediate magnification).
●● Patients may also manifest with gingival disease (linear gingival

erythema, necrotizing ulcerative gingivitis), periodontitis, and
aphthous ulcers.
●● Neoplasms likely to be encountered in this setting include
HPV-related squamous cell carcinoma, Kaposi sarcoma, and
lymphoma.
Salivary Gland Lesions

●● Many HIV-infected patients may present with enlargement of
their salivary glands, typically of the parotid, due to benign lym-
phoepithelial cysts (BLECs), intraparotid lymphadenopathy,
Salivary Gland Lesions 307
Fig. 13.3. Oral hairy leukoplakia. (Top) Patient with white patches shown
on the side of the tongue. (Bottom) Oral smear showing EBV infected
epithelial cells with prominent nuclear beading (Pap stain, high magni-
fication) (photographs courtesy of Dr. Shabnum Meer, Division of Oral
Pathology, University of the Witwatersrand, South Africa).
or less often infection (e.g., Cryptococcus, CMV sialadenitis,

mycobacteria) and neoplasia.
●● BLEC is bilateral in up to 20%. FNA yields straw-colored or
turbid fluid with or without a residual mass after aspiration. Cyst
aspiration is both diagnostic and therapeutic. On FNA, there is
a triad of (1) polymorphous reactive lymphoid cells, (2) cyst
contents with foamy histiocytes and proteinaceous background,
and (3) occasional epithelial cells (squamous, metaplastic, or
glandular including ciliated and mucinous types). The differen-
tial diagnosis includes branchial cleft cyst, Sjőgren syndrome,
Warthin tumor, and non-Hodgkin lymphoma.
●● Diffuse infiltrative lymphocytosis (DILS) presents in HIV-
infected patients with a Sjőgren-like syndrome of dry eyes and
mouth and salivary gland enlargement. The salivary glands
and several other body sites (e.g., lacrimal glands, kidney,
lung, gastrointestinal tract, and breast) are infiltrated by CD8+
T-lymphocytes. There is an increased risk of lymphoma and
some authors recommend follow up by FNA.
Lymphoproliferative Disorders
Posttransplant Lymphoproliferative
Disorder (PTLD)
●● PTLD is a well-recognized complication of transplantation.
Most cases are observed in the first year after transplanta-
tion. The greater the immunosuppression, the higher the inci-
dence of PTLD and the earlier it occurs.
●● In most cases, PTLD is associated with EBV infection of B-cells.
Therefore, evaluation of tumor for the presence of EBV is very
important, and can be accomplished by demonstrating the pres-
ence of EBV-encoded RNA (EBER) using in situ hybridization
in tumor cells.
●● EBV is uncommon with PTLD that presents in adults, late after
transplantation, tumors that are monomorphic, and more resist-
ant to treatment. PTLD of T-cell and NK-cell phenotypes is also
usually not associated with EBV infection, and does not respond
to immunosuppression dose reduction. Hence, it carries an unfa-
vorable prognosis.
Lymphoproliferative Disorders 309
●● The World Health Organization (WHO) classification for

the pathological diagnosis of PTLD includes four categories:
(1) early lesions (plasmacytic hyperplasia, infectious mononu-
cleosis-like lesion), (2) polymorphic PTLD, (3) monomorphic
PTLD (classified according to the B-cell or T-cell lymphoma that
it resembles), and (4) classical Hodgkin lymphoma-type PTLD.
AIDS-Related Lymphomas (ARL)

●● Lymphomas are an AIDS defining condition, except for low
grade B-cell lymphomas and Hodgkin lymphoma. AIDS-related
lymphomas (ARL) are divided by the WHO into three catego-
ries:
Lymphomas also occurring in immunocompetent patients:
Burkitt lymphoma, diffuse large B-cell lymphoma, extran-

odal marginal zone B-cell lymphoma of mucosa-associated
lymphoid tissue type, peripheral T-cell lymphoma, and Hodg-
kin lymphoma.
Lymphomas occurring more specifically in HIV-infected
patients: Primary effusion lymphoma (PEL) and plasmablas-

tic lymphoma.
Lymphomas also occurring in other immunodeficiency states:
Polymorphic or PTLD-like B-cell lymphoma.
Plasmablastic Lymphoma
●● This is an aggressive lymphoma that is EBV-associated (EBER-
positive, LMP-negative).
●● Tumors commonly present in the oral cavity, but have been
described in many other sites. Two subtypes have been described:
(1) oral mucosa type and (2) plasmablastic lymphoma with plas-
macytic differentiation.
●● Lymphoma cells (plasmablasts) are large, round to oval with
abundant cytoplasm, a paranuclear hof, eccentrically situated
nuclei, and single or multiple nucleoli. They often mimic other
poorly differentiated neoplasms including carcinoma. There
may be associated background apoptosis and tingible body
macrophages.
●● Tumor cells are positive for plasma cell markers (CD138, CD38,
MUM1), CD79a, CD30, and EMA. They may be negative or
weakly positive for CD45 (LCA), CD20, and PAX5.
Human Herpesvirus-8 (HHV8)-Associated

Lymphomas
●● These lymphomas include classic (body cavity based) PEL and
the solid (extracavitary) variant of PEL. Classic PEL presents with
effusions (pleural, peritoneal, pericardial, and rarely CSF or joint
space) and no mass or nodal disease. Solid PEL may manifest
with an effusion in addition to nodal or solid tissue lymphoma.
●● The cytology of either PEL subtype is characterized by large
atypical lymphoid cells ranging in appearance from immunob-
lastic to anaplastic phenotype (Fig. 13.4).
●● In most cases, PEL cells lack B-cell and T-cell markers, but
coexpress CD30, EMA, plasma cell antigens (CD38, CD138,
MUM-1) and HHV8.
●● PEL is associated not only with HHV8, but also sometimes with
EBV infection. HHV8 immunoreactivity can be very helpful in
diagnosing HIV-associated lymphomatous effusion (Fig. 13.5).
Hodgkin Lymphoma
●● Hodgkin lymphoma is currently among the most common non-
AIDS defining cancer (NADC) encountered, particularly the
mixed cellularity and lymphocyte-depleted subtypes.
●● Approximately 75–100% of these AIDS-associated cases have
EBV coinfection.
●● In HIV patients, Hodgkin lymphoma may be widely dissemi-
nated with frequent extranodal disease, but rare mediastinal
involvement.
Central Nervous System Disease

●● Meningitis. The etiology of meningitis in HIV-infected patients
is multifactorial and includes infection, inflammatory condi-
tions (e.g., IRIS), CNS lymphoma, and HIV itself.
Central Nervous System Disease 311
Fig. 13.4. Primary effusion lymphoma. (Left) CT scan images show a

large pericardial effusion in a 44-year-old HIV+ man who presented with
fever and cardiac tamponade. Over 1 L of fluid was drained. (Right) The
pericardial fluid shows large anaplastic lymphoma cells (Wright-Giemsa
stain, high magnification) that were immunoreactive with the LNA-1 anti-
body for HHV8. (Images reproduced with permission from Braza JM, Sul-
livan RJ, Bhargava P, Pantanowitz L, Dezube BJ. Images in HIV/AIDS.
Pericardial primary effusion lymphoma. AIDS Read. 2007;17(5):250–2.
Courtesy of UBM Medica).
Cryptococcal meningitis is the most common opportunistic

infection causing meningitis in HIV-infected individuals.
Other invasive fungal infections (Aspergillus, Candida) are
also important pathogens, especially in HIV-negative persons
with an immune deficiency.
Mycobacterial infection, coccidiomycosis, histoplasmosis,
candidiasis, and syphilis produce meningitis more frequently

in HIV-positive persons compared to HIV-negative patients.
Viral infections like CMV can cause meningoencephalitis.
Bacteria such as meningococci and pneumococcal meningitis
carry a high risk of mortality in HIV-infected people.

Fig. 13.5. Algorithmic approach to HIV-associated lymphomatous effu-

sions. BL Burkitt lymphoma; DLBCL diffuse large B-cell lymphoma;
HHV8 human herpesvirus-8; HL Hodgkin lymphoma; NHL non-Hodgkin
lymphoma; PAL pyothorax-associated lymphoma; PEL primary effusion
lymphoma (reproduced with permission from Pantanowitz L, Dezube BJ.
HIV-related lymphomas. Int Pleural Newslett. 2009;7:18–9).
●● Mass lesions. Space occupying lesions in the HIV positive patient

may be due to infections such as toxoplasmosis, mycobacteria,
and cryptococcus, as well as neoplasms such as primary CNS
lymphoma (PCNSL) and metastases.
Toxoplasmosis is characterized radiologically by multiple
enhancing brain lesions. The diagnosis is often misdiag-

nosed in intraoperative cytology specimens because the par-
asites are easily overlooked. They are typically seen within
pseudocysts (bradyzoites). This should be kept in mind when
there are nonspecific changes with an atypical lymphocytic
infiltrate.
PCNSL is associated with EBV. The cytomorphology of this
B-cell lymphoma is that of a diffuse large B-cell lymphoma.

Central Nervous System Disease 313
●● Progressive multifocal leukoencephalopathy (PML). This is a

subacute demyelinating disorder due to JC virus, a polyomavirus
that targets oligodendrocytes. JC virus reactivates in conditions
of immune suppression.
Neuroimaging findings together with CSF analysis for JC
viral antigen using PCR are usually diagnostic.

Routine cytologic CSF analysis is typically normal. FNA
samples and brain smears may reveal foci of white matter

demyelination, eosinophilic inclusions in oligodendrocytes,
and abnormal giant astrocytes.
In equivocal cases, stereotactic brain biopsy provides a defin-
itive diagnosis (Figs. 13.6 and 13.7).
Fig. 13.6. AIDS-associated brain toxoplasmosis. (Left) An intraoperative

smear shows a “bag of parasites” (arrow) among scattered chronic inflam-
matory cells (H&E stain, high magnification) that (right) can also be seen
in the brain surgical biopsy specimen (H&E stain, high magnification).
Toxoplasma infection was confirmed using immunohistochemistry.
Fig. 13.7. Progressive multifocal leukoencephalopathy (PML). (Top left)

Brain smear showing reactive gliosis and foam cells (H&E stain, interme-
diate magnification). (Top right) Oligodendrocyte (arrow) with a ground
glass intranuclear inclusion (H&E stain, high magnification). (Bottom
left) Enlarged astrocyte with a bizarre nucleus is shown among several
background foamy macrophages (H&E stain, high magnification). (Bot-
tom right) Infected cells show strong positive staining with a JC virus
immunostain (high magnification) (image courtesy of Dr. Clayton A.
Wiley, Neuropathology, University of Pittsburgh Medical Center, USA).
Pulmonary Disease
●● Infection. Specific microorganisms likely to be encountered
include conventional causes of bacterial pneumonia, mycobac-
terial infection, P. jirovecii, Cryptococcus neoformans, and various
viral infections (e.g., CMV, HSV).
A potential pulmonary pathogen may be identified in approxi-
mately 25% of HIV+ individuals with negative BAL cytology

using other diagnostic modalities (e.g., culture, biopsy).
Uncommon infections have been reported in AIDS patients
such as microsporidiosis and malakoplakia associated with

Rhodococcus equi.
Pulmonary Disease 315
Fig. 13.8. Tuberculous (TB) effusion. An effusion in an HIV+ patient is

shown with mature lymphocytes, serous material, and a dearth of mes-
othelial cells. Culture of the fluid revealed Mycobacterium tuberculosis
(Pap stain, low magnification).
●● Neoplasia. Lung tumors that may be seen in HIV+ patients

include Kaposi sarcoma, lymphoma, and carcinoma.
Lung carcinoma in HIV+ patients is predominantly adeno-
carcinoma, which tends to present at a younger age and with

more advanced stage than in HIV-negative people.
●● Effusions. Pleural effusion in HIV-infected patients is common,
with a prevalence of 14–27%.
The etiology may include infections (parapneumonic effu-
sions, mycobacteria, empyema, CMV, P. jirovecii), neoplasia

(mainly Kaposi sarcoma and lymphoma), and miscellaneous
conditions (e.g., fluid overload, hypoalbuminemia, nephropa-
thy, chronic liver disease, and pulmonary embolism).
Macroscopically, a mycobacterial effusion yields shiny green
fluid that contains very few mesothelial cells (Fig. 13.8) and
typically increased numbers of lymphocytes (often >50%
lymphocytes). In HIV+ patients an AFB smear may be positive
in ~20% of cases, with pleural fluid culture positive in many

more (40%) specimens. Pleural fluid adenosine deaminase
(ADA) levels are often elevated.
Mesothelial cells in recurrent pleural effusions from patients
with AIDS-associated Kaposi sarcoma and Castleman dis-

ease may be infected with HHV8.
Renal Disease
●● BK polyomavirus infection in immunocompromised individuals
can cause renal dysfunction and abnormal urine cytology (cov-
ered in Chap. 8).
●● In some (1–10%) renal transplant recipients, BK virus may
infect and replicate within the renal graft (called BK nephropa-
thy). As a result, up to 80% of these patients may lose their renal
grafts. Nephritis can arise soon (within days) after transplanta-
tion to as late as 5 years.
●● In bone marrow transplant patients, BK virus is a frequent cause
of hemorrhagic cystitis.
Spindle Cell Lesions

Specific spindle cell lesions that should be considered in the setting
of immunosuppression include the following:
●● Mycobacterial spindle pseudotumor. These lesions contain spindle-
shaped macrophages (CD68+) that harbor numerous mycobac-
teria (AFB positive). They predominantly involve lymph nodes,
but may affect the skin and bone marrow. They are most often
associated with atypical mycobacteria like Mycobacterium
avium intracellulare (MAI).
●● Kaposi sarcoma. Aspirates procured from these lesions contain
clusters and bland spindle cells (CD34+, CD31+, D2-40+) present
in a bloody background. Nuclear immunostaining with LNA-1
for HHV8 (KSHV) is diagnostically helpful in these cases.
●● EBV-associated mesenchymal tumors. Leiomyoma, leiomy-
osarcoma, and myopericytoma present with spindle cells that
Spindle Cell Lesions 317
are positive with smooth muscle markers and EBER by in situ

hybridization. In HIV+ patients, these tumors usually occur in
unusual sites and may be multifocal.
●● Follicular dendritic cell sarcoma. These neoplasms can present
in nodal and extranodal sites. An association with EBV has been
shown in some cases. Neoplastic spindle to ovoid cells show
morphologic and phenotypic features of follicular dendritic
cells (positive for CD21, CD35, CD23, clusterin, and fascin)
(Figs. 13.9 and 13.10).
Fig. 13.9. HIV-associated spindle cell lesions. (Top left) FNA from a
neck lymph node showing LNA-1 negative spindle cells arranged in a
large cluster. Culture revealed Mycobacterium tuberculosis confirming
the diagnosis of Mycobacterial spindle cell pseudotumor (Pap stain, inter-
mediate magnification). (Bottom left) Kaposi sarcoma spindle cell nuclei
stain positively with LNA-1 confirming HHV8 infection (immunostain,
high magnification). (Right) Lung FNA from an HIV+ male showing
loose aggregates of spindle cells with eosinophilic cytoplasm and nuclear
atypia in a necrotic background. Ancillary investigations confirmed the
presence of a leimyosarcoma (Pap stain, intermediate magnification).
Fig. 13.10. Follicular dendritic cell sarcoma showing fascicles and sheets
of atypical spindle cells with moderate amounts of cytoplasm, finely
granular chromatin, and small nucleoli (Pap stain, left intermediate mag-
nification, right high magnification).
Suggested Reading
Ellison E, Lapuerta P, Martin S. Fine needle aspiration (FNA) in HIV+
patients: results from a series of 655 aspirates. Cytopathology.
1998;9:222–9.
Gattuso P, Castelli MJ, Peng Y, Reddy VB. Posttransplant lymphopro-
liferative disorders: a fine-needle aspiration biopsy study. Diagn
Cytopathol. 1997;16:392–5.
Hanks D, Bhargava V. Fine-needle aspiration diagnosis of HIV-related
conditions. Pathology. 1996;4:221–52.
Kocjan G, Miller R. The cytology of HIV-induced immunosuppression.
Changing pattern of disease in the era of highly active antiretroviral
therapy. Cytopathology. 2001;12:281–96.
Lobenthal SW, Hajdu SI. The cytopathology of bone marrow transplanta-
tion. Acta Cytol. 1990;34:559–66.
Michelow P, Meyers T, Dubb M, Wright C. The utility of fine needle
aspiration in HIV positive children. Cytopathology. 2008;19:86–93.
Spindle Cell Lesions 319
Naresh K. Lymphoproliferative disorders in the immunosuppressed.

Diagn Histopathol. 2009;16:206–15.
Pantanowitz L, Dezube BJ. Evolving spectrum and incidence of non-
AIDS-defining malignancies. Curr Opin HIV AIDS. 2009;4:27–34.
Pantanowitz L, Kuperman M, Goulart RA. Clinical history of HIV infec-
tion may be misleading in cytopathology. Cytojournal. 2010;7:7.
Pantanowitz L, Michelow P. Review of human immunodeficiency virus
(HIV) and squamous lesions of the uterine cervix. Diagn Cytopathol.
2011;39:65–72.
Siddiqui MT, Reddy VB, Castelli MJ, Gattuso P. Role of fine-needle aspi-
ration in clinical management of transplant patients. Diagn Cytopathol.
1997;17:429–35.
hgbjkdfg
14
Ancillary Investigations
Pam Michelow1, Tanvier Omar2,
1
2
Division of Cytopathology, Department of Anatomical Pathology, School of
Pathology, National Health Laboratory Service, and University of
Witwatersrand, Johannesburg, Gauteng, South Africa
3
Cytomorphology alone using routine stains such as the Papanicolaou

(Pap), Diff-Quik (DQ), and hematoxylin and eosin (H&E) stains
may be adequate to diagnose several infections in cytology mate-
rial. However, the use of ancillary investigations improves cyto-
logic diagnostic accuracy, may help subtype microorganisms, and
determine their antimicrobial sensitivity. Identification of infec-
tious organisms by the laboratory relies primarily on microscopy,
special stains (histochemistry and immunocytochemistry), and
culture. With the well-established success of cell block technique,
many cytology samples can now be effectively stained using immu-
nocytochemistry. A fresh specimen may not always be available
to submit for microbiology culture. In addition, culture may have
limited utility in some clinical cases due to the prolonged incuba-
tion required for the growth of fastidious pathogens and the ina-
bility to culture others. While microscopy and culture techniques
remain very useful, newer detection methods are being introduced
into routine clinical practice such as in situ hybridization (ISH),
flow cytometry, and molecular tests. One of the best examples in
cytopathology of new technologies being rapidly incorporated

322 14. Ancillary Investigations
into laboratory diagnostic tests is for the detection of human

papillomaviruses (HPV). HPV testing technologies can be divided
into four main types of methods: (1) direct probe methods (Southern,
dot blot, and ISH), (2) signal amplification system (hybrid capture),
(3) target amplification system (polymerase chain reaction [PCR],
nuclei acid sequence-based amplification), and (4) emerging
technologies (microarrays).
Routine Cytology Stains

Papanicolaou (Pap) Stain
●● The Pap stain is the most widely used routine cytologic stain
applied to alcohol-fixed material. Hematoxylin is used as a
nuclear stain and Orange G-6 (OG-6) and eosin-azure (EA) as
cytoplasmic counterstains. This stain is not entirely standard-
ized and slight differences exist in dye composition and stain
technique.
●● The Pap stain provides good nuclear and cytoplasmic details
of many organisms, in addition to the host’s cellular changes
like inflammation, repair, and neoplasia that may be induced by
the infective process. Most viral changes including nuclear and
cytoplasmic inclusions are best seen in Pap-stained smears.
Romanowsky Stains
●● Romanowsky stains are applied to air-dried smears and blood
smears. Several different types of Romanowsky stains exist
(e.g., DQ, May-Grunwald and Giemsa [MGG]), but all are
based on a combination of reduced eosin, methylene blue, and
thiazine dyes.
●● Romanowsky stains are used, for the most part, to stain cyto-
plasm, and extracellular substances. Bacteria, fungi, and para-
sites are often easier to detect on Romanowsky, as compared to
Pap, stained smears. They also allow one to identify the nega-
tive image (unstained element) of certain microorganisms (e.g.,
mycobacteria) if present.
Special Stains 323
Hematoxylin and Eosin (H&E) Stain

●● The H&E stain consists of hematoxylin and eosin. Most cytology
laboratories reserve H&E for staining cell blocks. H&E stains
are also occasionally used for intraoperative cytology prepara-
tions (e.g., touch or squash preparations).
●● Like the Pap stain, the H&E stain provides good nuclear and cyto-
plasmic details of many organisms, in addition to the host’s cel-
lular changes stimulated by infection. OG-6 is not present in the
H&E stain, limiting the detection of keratin in squamous cells.
Toluidine Blue
●● Toluidine blue is a rapid stain for use on fresh specimens to
assess specimen adequacy.
●● Some organisms (e.g., Pneumocystis jirovecii) can be readily
identified with Toluidine blue staining, allowing the specimen
to be placed in the appropriate microbiologic medium for best
culture results.
Cell Blocks
●● Cell blocks are created by placing cytology material into a fixa-
tive, of which several are available such as 10% buffered for-
malin. The liquid specimen is centrifuged to create a cell pellet,
which is embedded for sectioning as for biopsy material.
●● Both conventional exfoliative and aspiration cytology have lim-
ited material available for ancillary investigations. The use of cell
block technique allows for many sections to be made and hence
multiple special stains and immunostains can be performed for
infectious diseases. Large structures floating in liquid-based
specimen vials may only be identified in cell block material.
Special Stains
●● Most staining methods available for formalin-fixed tissues can be
successfully adapted for cytology smear and cell block material.
●● With the exception of acid-fast and Gram stain where air-dried
material is preferred, the stains described below are better
p erformed on alcohol-fixed material. If only air-dried material is

available, prior rapid fixation for 10 s in 95% alcohol is advised
to ensure that material does not wash off during staining.
●● Routinely stained slides can be used for special stains if needed,
but require decolorization in acid alcohol for 2–10 minutes prior
to the specific staining process.
●● Positive controls should be run with each test. While it is pref-
erable to use cytology specimens as controls, this is often not
possible due to the limited number of available cytology slides.
Formalin-fixed tissue sections are more easily available and
serve as useful substitutes.
Wet Mount Preparation

●● A saline (0.85% NaCl) wet prep may be used to detect the micro-
scopic presence of various microorganisms in liquid specimens.
The prep is observed using brightfield microscopy. Material
must usually be examined within 30 min once obtained. It can
be used on vaginal secretions to diagnose motile Trichomonas
vaginalis trophozoites, clue cells, and yeast.
●● A wet prep with 20% potassium hydroxide (KOH) lyses epi-
thelial cells allowing for easier visualization of certain micro-
organisms (e.g., Candida). Placing a drop of KOH on a slide of
the wet prep may cause a foul, fishy odor if there is anaerobic
overgrowth or infection (known as the “whiff” test).
Bacterial Stains
Gram Stain
●● The Gram stain differentially stains Gram positive and Gram
negative bacteria. It is well suited for use with air-dried smears.
●● The differential staining results from differences in the chemical
(peptidoglycan) composition and thickness of the cell walls of
Gram positive and Gram negative organisms.
●● There are four basic steps of the Gram stain: (step 1) apply a
primary stain (crystal violet or methylene violet); (step 2) add
a trapping agent (Lugol’s iodine); (step 3) rapid decolorization
Bacterial Stains 325
Fig. 14.1. Gram stained bacteria (Gram stains, high magnification). (Left)
Clusters of Gram positive Staphylococcus aureus cocci are shown in this
specimen from an infected skin wound. (Right) Numerous Gram negative
Haemophilus rods and coccobacilli are present in the background among
neutrophils and bronchial cells in this bronchoalveolar lavage specimen.
with alcohol or acetone; and (step 4) counterstain with safranin

(or neutral red).
●● Gram negative bacteria stain red and Gram positive bacteria
appear blue-black. The age of bacteria, antibiotic treatment, fra-
gility of the cell wall, over-decolorization, and decalcification
may cause Gram positive bacteria to appear Gram negative.
●● Other microorganism may also stain. For example, fungi like
Candida albicans and cryptococcus as well as intracellular
microsporidia stain gram positively.
●● Modified Gram stains like the Brown and Hopp’s or Gram-
Twort stains are better suited for use with formalin-fixed tissue
sections. These methods should be employed when staining of
cell block material is required.
●● Caution: Crystal violet is toxic when swallowed and in vapor
form causes ocular irritation. Iodine is a corrosive and can cause
cutaneous burns (Fig. 14.1).
Stains for Helicobacter pylori

●● In cytology laboratories where gastric washing cytology is regu-
larly assessed, special staining for H. pylori may be necessary.
Several staining methods can be employed:
●● Cresyl violet acetate: This rapid, simple stain employs no

counterstain. H. pylori organisms stain purple. The background
stains in lighter hues of the same color. This will also stain
Pneumocystis cysts.
●● Gimenez: This stain is good for slow-growing and fastidi-
ous bacteria. The stain uses carbol fuchsin to stain the organ-
isms a magenta color. The counterstain with 1% malachite
green achieves a blue-green background. This staining proc-
ess requires steps and care should be taken not to overstain the
background. Gimenez can also be used to highlight Legionella
bacilli.
●● Toluidine blue: This reliable metachromatic stain uses a phos-
phate buffer at pH 6.8 to stain H. pylori dark blue. The back-
ground stains a lighter shade. Toluidine blue also stains
Pneumocystis cysts.
●● Silver stains: Other stains sometimes used include silver stains
such as Warthin–Starry, Genta, or Steiner methods.
●● Specific immunocytochemistry can also aid in bacterial detec-
tion. It is highly specific and has a higher sensitivity than bac-
teriological culture and other classical histological staining
methods.
Warthin-Starry Stain
●● This is a fastidious stain used for identifying spirochetes, Bar-
tonella henselae and Bartonella quintana, Donovan bodies, and
H. pylori. It is also capable of demonstrating Klebsiella and
Leptospira bacteria as well as microsporidia, although this is
rarely indicated.
●● The stain employs a silver heat impregnation technique. Once
silver salts deposit onto the organisms, they are reduced with
hydroquinone to produce a silver metal.
●● Microbes appear somewhat magnified and stain black in a
golden brown background.
●● Stains with necrotic material or cells with intracellular debris
that show nonspecific staining are difficult to interpret. The
incubation step of this stain is critical to provide a well-stained
slide. Over- or underdeveloped sections are frustratingly diffi-
cult to interpret. Nonspecific precipitation can be removed by
rapid rinsing in 2.5% iron alum.
Fungal Stains 327
●● Dieterle stain is another silver impregnation stain that can be

used to identify similar organisms as for the Warthin-Starry
stain, and may also stain Mycobacterium tuberculosis.
Acid-Fast Stains for Mycobacteria (AFB)

●● These stains are preferentially performed on air-dried material
to prevent alcohol disruption of bacterial cell walls.
●● The lipid capsule of mycobacteria is hydrophobic, rendering
them resistant to Gram staining. However, these bacteria can
be stained using concentrated dyes, particularly when the stain-
ing process is combined with heat. Once stained, these microor-
ganisms resist a dilute acid and/or ethanol-based decolorization
procedure. Hence, once stained, the mycobacterial capsule is
acid, and variably alcohol-fast. This chemical property forms
the basis of the various acid-fast stains (Table 14.1).
●● It is advisable to use a fairly pale methylene blue counterstain
to enhance visualization of bacilli, especially since some myco-
bacteria are often sparse.
●● Mycobacteria may also stain with other stains. For exam-
ple, Mycobacterium spp. are also Grocott methanamine silver
(GMS) positive and Mycobacterium avium-intracellulare com-
plex (MAC) stains with periodic acid-Schiff (PAS).
●● Modified AFB stains can also stain Nocardia, Rhodococ-
cus, Legionella micdadei, the spines on Schistosoma spp. ova,
Echinococcus hooklets, and Cryptosporidium spores (Figs. 14.2
and 14.3).
Fungal Stains
●● Fungi are usually visualized as spores and/or hyphae. Specific
host responses together with the size, septation, budding, and
branching characteristics of these fungal elements assist in
fungal speciation.
●● Factors that may influence the appearance of fungal elements
include the age of the fungal lesion, effects of antifungal therapy,
type of infectious tissue, and host immune response.
●● Fungi possess polysaccharide-rich cell walls. The oxidation
of these carbohydrate components to dialdehydes forms the
Table 14.1. Acid-fast stains for mycobacteria.

Stain Action Result
Auramine- Constituent fluorochromes Bacilli fluoresce orange-
rhodamine bind to cell wall yellow in a black
background under
ultra-violet light
Ziehl-Neelsen Phenol facilitates staining Mycobacteria stain red to
of cell walls with carbol fuchsin, purple and are slightly
resisting decolorization by strong curved, rod shaped
acid alcohol. Heat is required bacilli, and occasion-
Kinyoun Modification of the Ziehl-Neelsen ally beaded
stain. Heat is not required and the
concentrations of carbol fuschin
and phenol are higher
Modified Fite Staining principle similar to Preferable for atypical
Ziehl-Neeslen. Peanut oil mycobacteria,
can be added to enhance acid- M. leprae, and
fastness. Acid alcohol is replaced Nocardia. Organisms
by sulfuric acid. Xylene is stain red
avoided to protect delicate
walls of atypical mycobacteria
Triff Combination of carbol fuschin, Utilized for M. leprae
Mayer’s hematoxylin to stain which stains red
nuclei, eosin yellow to stain cyto-
plasm, and alcohol saffron
as a counterstain
basis of PAS and GMS stains (Table 14.2). GMS is preferred

for screening, because it gives better contrast and stains even
degenerated and nonviable fungi. Overstaining with GMS pre-
vents the internal structure (e.g., hyphal septae) to be visualized.
Mucormycosis may be only weakly positive for GMS. Histo-
plasma capsulatum organisms are not adequately demonstrated
by the PAS reaction.
●● The cell wall or capsule of several fungi will stain with mucicar-
mine, including Cryptococcus, Blastomyces, and Rhinosporid-
ium. In some cases, poorly encapsulated or capsule-deficient
cryptococci may not stain positively with mucicarmine stain.
Alcian blue can also demonstrate the mucoid capsule of
Cryptococcus neoformans.
Fig. 14.2. A Ziehl-Neelsen stain demonstrating acid-fast bacilli (AFB) that
on culture proved to be Mycobacteria tuberculosis (high magnification).
Fig. 14.3. Modified Fite stain demonstrating Mycobacteria leprae (high

magnification) (image courtesy of Dr. Pawel Schubert, University of
Stellenbosch, Cape Town, South Africa).
330
14.
Table 14.2. Characteristics of routinely used fungal stains.

Stain Action Fungi Comment
McManus periodic Schiff’s reagent stains glycogen Useful for a variety of fungi including Basic fuschin is carci-
acid-Schiff (PAS) and fungal cell walls oxidized by Candida, Cryptococcus, Histoplasma, nogenic and direct
periodic acid magenta. Mayer’s Aspergillus, Mucormycosis, and contact or inhalation is
hematoxylin is used to stain nuclei. Blastomycosis. Also highlights rabies viral best avoided
Light green may be used as a inclusions and mycobacteria when present
counterstain in large numbers
Grocott methanamine Polysaccharide cell walls are Highlights fungal cell walls and Over-incubation and
silver (GMS) oxidized in chromic acid to Pneumocystis jirovecii cysts. Some bacteria, uneven temperatures
expose aldehydes prior to silver actinomycetes and Nocardia stain result in distortion
impregnation. Light green or brown-black. Useful in staining carbohydrate of internal fungal
H&E can be used as a counterstain centers of dead mycobacteria where cell morphology
wall integrity is compromised. Also stains
E. histolytica, encysted amoebas, CMV
intracytoplasmic inclusions, echinococcal
cyst wall and algae
Stains for Rickettsia 331
Fig. 14.4. Fungal stains (high magnification). (Upper left) PAS high-
lighting Cryptococcus in an FNA of a lymph node. (Bottom left) GMS
demonstrates Pneumocystis jirovecii cysts in an alveolar cast from a bron-
choalveolar lavage. (Upper right) Mucicarmine highlights several encapsu-
lated C. neoformans yeast. Note the narrow-based budding of an organism
in the upper center of the image. (Bottom right) Lactol-phenol cotton blue
stain is used to illustrate Aspergillus flavus isolated from fungal culture.
●● Fontana-Masson stain may demonstrate the cell wall of C. neo-

formans and also stains all dematiaceous (pigmented) fungi
(e.g., Phaeohyphomycosis).
●● Lactol-phenol cotton blue (LPCB) staining is used to examine
fungal cultures in the mycology laboratory. It is also used to
detect acid-fast parasites in stool and gastrointestinal aspirate
specimens (Fig. 14.4).
Stains for Rickettsia

●● Rickettsial infections are caused by small Gram negative
obligate intracellular coccobacilli transmitted by ticks, fleas,
lice, and mites. In humans, the organisms invade and multiply
in vascular endothelium. Multi-organ involvement can occur.

Diagnosis of an infection is usually made by complement
fixation, immunofluorescence, or PCR of tissue or blood.
●● While their visualization is rarely required in cytology, they can
be seen with Romanowsky stains or by means of Macchiavello’s
stain.
Stains for Viruses

●● Several viral infections often result in morphologically visible
cytopathic effects that permit a diagnosis to be made in conven-
tionally stained cytological preparations. Viral inclusions may
be nuclear and/or intracellular. Table 14.3 lists several stains
available for viral infections.
●● The increasing availability of monoclonal antibodies and
hybridization probes to detect viruses has made the use of spe-
cial stains less popular (Fig. 14.5).
Stains for Parasites

●● The diagnosis of protozoal infections has been simplified by the
availability of new diagnostic modalities including serological
agglutination tests, immunohistochemistry, immunofluores-
cence, and PCR. Moreover, in cytological material, protozoal
morphology can usually be appreciated on routine staining.
●● The preferred stain for blood parasites is a Giemsa stain.
●● Tri-PAS is a useful stain to confirm the presence of amoeba in
cytology smears. It extends the conventional PAS stain by add-
ing a Mayer’s hematoxylin counterstain and orange G to dem-
onstrate erythrophagocytosis. Ameba are weakly hematoxyphilic
and color pinkish orange. Engulfed red cells stain orange.
●● Ova in schistosomiasis stain readily with H&E, Pap, GMS, and
Ziehl-Neelsen stains. For echinococcosis (hydatid disease), the
laminated membrane can be highlighted by PAS or GMS stains,
and the refractile hooklets can be illustrated with a modified
Fite stain.
●● Fecal material for microbiology specimens is stained with Tri-
chrome, iron hematoxylin, and/or modified acid-fast stains.
Table 14.3. Stains for viral infections.
Stain Action Positive result Comment
Macchiavello Basic fuchsin is differentiated with citric Viral inclusions (e.g., Negri bodies Organisms stain red and tissue
acid and counterstained with methylene blue in rabies), rickettsia and chlamydia cells blue
Lendrum’s phloxine- Trichrome stain that uses hematoxylin to Molluscum contagiosum Russell bodies, keratin, Paneth
tartrazine stain nuclei blue, phloxine to stain viral and measles cells are resistant to tartra-
inclusions bright red and tartrazine to serve zine differentiation and may
as a differentiator be a source of false-positive
interpretation
Shikata’s Orcein Potassium permanganate oxidizes sulfur Hepatitis B surface antigen is Orcein should be freshly
containing proteins to form sulfonate demonstrated in the cytoplasm of prepared each week
residues which react with orcein. Rectified hepatocytes. Infected cells stain
spirits are used to differentiate dark red or brown in a light brown
background
Feulgen Acid hydrolysis with hydrochloric acid Cytomegalovirus inclusions stain This is an uncommonly used
breaks down DNA bonds in nuclear material. magenta stain for the demonstration
The exposed nucleic acid components of DNA
are stained using the PAS stain
Tzanck smear Smear of blister fluid in herpes virus infection Highlights herpes cytopathic Sensitivity is lower if the her-
stained with a Pap or H&E stain effect (HSV I and II, VZV) petic lesion has crusted
and nonherpetic findings
Stains for Parasites
333
Fig. 14.5. Phloxine-tartrazine stain demonstrating multinucleated cells

with viral nuclear and cytoplasmic inclusions staining red consistent with
measles infection in this lung FNA (high magnification) (image courtesy of
Dr. Pawel Schubert, University of Stellenbosch, Cape Town, South Africa).
Immunocytochemistry
●● Immunocytochemistry uses antibodies to detect the presence
of proteins or antigens in cells and tissues. The material to be
tested can be smears, imprints, cytospin cell suspensions on
glass slides, or cell blocks. Cell blocks are preferred for immu-
nocytochemistry as they allow for optimal antigen retrieval.
However, alcohol-fixed and air-dried material can be success-
fully used with some modifications.
●● Where smears, imprints, and cytospins are being prepared spe-
cifically for immunocytochemistry, they should preferably be
air-dried prior to fixation in acetone using charged/adhesive
slides. Acetone is less destructive of tissue epitopes than alco-
hol, and will allow for superior antigen retrieval.
●● All alcohol-fixed material should be decolorized in acid-alcohol
before being postfixed in 10% buffered formalin for 30 seconds
In Situ Hybridization 335
followed by incubation in 0.25–0.5% Triton X-100 in PBS for

10 minutes to permeabilize cell membranes. This step can be
omitted following acetone or methanol fixation. This is followed
by routine staining as per the manufacturer’s instructions.
●● Immunocytochemistry is useful where microorganism specia-
tion is needed and there is no fresh tissue for culture available,
or culture will take too long for a diagnosis. It is also useful in
cases with atypical morphology or unusual presentation of an
infectious disease.
●● Immunochemistry for diagnosing infectious diseases is expand-
ing as the number of commercial antibodies available for use
increases. Immunostains allow for the confirmation of morpho-
logical observations, especially where the cytological features
are not definitive. It is particularly useful for rapid diagnoses in
cases where culture is not available or too time consuming. To
date, antibodies to a range of bacterial, mycobacterial, viral, fun-
gal, and parasitic organisms have been developed (Table 14.4).
These immunostains are often more sensitive and specific than
their special stain counterparts (Figs. 14.6–14.8).
In Situ Hybridization
●● ISH utilizes a complementary and known DNA or RNA strand
(probe) to localize a specific DNA or RNA sequence. Several
different methods are used to identify the hybridized probe-
target complex including fluorescent tags (FISH), chromagens
(CISH), and nonisotopic labeling systems (NISH). PCR can
then be used to amplify the DNA or RNA sequences obtained
using ISH.
●● Fresh or destained archival material can be utilized for FISH,
although destained archival material yields less consistent
results. Air-dried and fixed smears including liquid-based prepa-
rations and paraffin-embedded cell blocks are suitable for ISH.
●● The advantage of ISH over immunocytochemistry is that the
actual gene product is identified rather than protein uptake or
receptor-bound proteins, reducing false-positive, and false-
negative results that may occur with immunocytochemistry. ISH
allows staining to be correlated with cellular morphology.
Table 14.4. Useful commercially available immunocytochemistry antibodies for microbe identification.
336
Microorganism Localization Comment
Actinomycetes Bacteria Antibodies for Actinomyces genus, A. israelii and A. naeslundii
14.
Adenovirus Nuclear Pan-adenovirus marker; monoclonal antibody is reactive with all 41 sero-
types of adenovirus
Aspergillus Fungal elements Genus specific only. Stains fungus cell wall, septa, and cytoplasm
Bartonella henselae Bacteria Polyclonal antibody that does not differentiate between B. henselae and
B. quintana. There is also a monoclonal antibody specific for B. henselae
BK virus Nuclear Specific for BK virus. The antibody is directed against the large T cell
antigen of SV40 virus
Candida albicans Fungal elements Does cross-react with other yeasts
Cryptococcus Fungal elements Stains different Cryptococcus neoformans and serotypes
Cytomegalovirus Nuclear and cytoplasmic No cross-reaction with other herpes viruses or adenovirus
EBV latent membrane protein Membranous and cytoplasmic Monoclonal antibodies to LMP-1 or LMP-2
Epstein Barr virus Nuclear Acetone fixed tissue only; replicating and latent infection (EBNA2)
Giardia intestinalis Extracellular Stains protozoa on luminal surface of epithelia
Helicobacter pylori Bacteria Also cytoplasmic staining
Hepatitis B core Ag Nuclear and cytoplasmic Targets core antigen in infected cells
Hepatitis B surface Ag Cytoplasmic Targets surface antigen in infected cells (HBsAg)
Hepatitis C virus Cytoplasmic Sensitivity variable
Herpes simplex virus 1 and 2 Nuclear and cytoplasmic Some cross-reactivity may be observed. Polyclonal antibody does not
distinguish between HSV-1 and HSV-2
Human Herpesvirus 8 Nuclear Targets latent nuclear antigen-1 (LNA-1); also called latent associated
nuclear antigen-1 (LANA)
Human immunodeficiency virus Granular staining close to Targets P24 protein. Not suited to tissues that have had prolonged fixation
infected cell in formalin
Human papilloma virus (HPV) Nuclear Major capsid protein antibody expressed in HPV type 6, 11, 16, 18, 31, 33,
42, 51, 52, 56 and 58
Merkel cell polyomavirus Nuclear Majority (not all) Merkel cell tumors are positive
Mycobacterium bovis Cell wall of organism Raised against BCG
Mycobacterium tuberculosis Cell wall of organism Species specific. With anti-BCG polyclonal antibody has shown better
sensitivity than AFB staining, except in cases where there are very few
bacilli. A polyclonal antibody against the M. tuberculosis-secreted anti-
gen MPT64 is also useful
Parvovirus B19 Nuclear and cytoplasmic Recognizes an epitope common to VP1 and VP2 proteins of human Parvo-
virus B19
Pneumocystis jiroveci Cyst wall Specific to P. jiroveci (formerly P. carinii). Stained rings correspond to
individual cyst walls
Prion protein Cytoplasmic Also called prion protein PrP antibody
Respiratory syncytial virus Cytoplasm and cell membrane There are multiple types and subtypes of RSV that may not be covered by
all clones
Toxoplasma gondii Parasites Stains bradyzoites and tachyzoites. Targets Toxoplasma gondii p30 surface
antigen
Varicella Zoster virus Cytoplasmic Specific for varicella zoster; does not cross-react
Zygomycoses Fungal elements Genus specific only
In Situ Hybridization
337
Fig. 14.6. Immunocytochemistry. (Left) A CSF specimen showing immu-

noreactive cryptococcal yeast (high magnification). (Right) Direct smear
of a Merkel cell carcinoma showing positive staining of tumor cells with
CM2B4, a monoclonal antibody to exon 2 peptides of the Merkel cell
polyomavirus (MCPyV) T antigen (intermediate magnification).
Fig. 14.7. Aspergillus immunocytochemistry. (Left) Multiple hyphae

of Aspergillus spp. are present with inflammatory cells in this cell block
from a bronchoalveolar lavage (PAS stain, intermediate magnification).
(Middle) Aspergillus hyphae in this BAL case are immunoreactive in cell
block material (intermediate magnification). (Right) Immunostains can
help identify rare branching Aspergillus hyphae as depicted in this lung
cytology specimen (high magnification). The commercially available
monoclonal antibody for aspergillosis usually detect several Aspergillus
spp. like A. fumigatus, A. flavus, and A. niger.
●● ISH is useful for the detection of a wide range of organisms

including viruses like human papillomavirus, cytomegalovi-
rus, hepatitis viruses, herpes simplex viruses, and Epstein-Barr
virus (EBV); bacteria such as Helicobacter pylori, legionella,
In Situ Hybridization 339
Fig. 14.8. Pap test immunocytochemistry. (Left) High grade squamous

intraepithelial cells (HSIL) are shown on a ThinPrep Pap test (Pap stain,
high magnification). (Right) These HSIL cells demonstrate p16 nuclear
and cytoplasmic immunoreactivity, a surrogate marker indicative of HPV
infection (high magnification). In dysplastic cells of the uterine cervix E7
protein of high-risk HPV inactivates retinoblastoma protein (pRB) which
in turn leads to the overexpression of p16.
and tuberculosis; and fungi such as blastomyces, coccidioides,

cryptococcus, histoplasmosis, sporothrix, and parasites includ-
ing malaria, cryptosporidium, and amebae.
●● For the detection of HPV, ISH allows for both the diagnosis of
integrated HPV, and visualization of HPV within these infected
cells. ISH is available for both low-risk and high-risk HPV types.
Low-risk HPV-related lesions (e.g., papillomas) often contain low
viral copy numbers, show only patchy staining, and may not be
uniformly positive for HPV. High-risk HPV-positive lesions and
tumors (e.g., HSIL) may show more diffuse positivity for HPV.
●● EBV-encoded RNA (EBER1 and EBER2) is expressed in cells
infected with EBV. ISH for EBER has been recommended as
perhaps the best test for detecting and localizing latent EBV in
tissue and cytology samples. False-positive EBER interpretations
may occur as a result of confusion related to latent infection of
background lymphocytes instead of lymphoma cells, nonspecific
staining, or cross-reactivity with mucin, yeast, or plant materials.
False-negative results may occur with RNA degradation.
●● Before concluding that a slide for ISH to localize is negative, it
is important to evaluate a control slide that was run in parallel,
demonstrating that RNA or DNA is present and available for
hybridization in the cells of interest (Fig. 14.9–14.11).
Fig. 14.9. HPV-ISH of a cervix condyloma. Tissue biopsy of this condy-

loma shows patchy positive nuclear staining for low-risk HPV in surface
koilocytes (low magnification).
Fig. 14.10. Infectious mononucleosis. (Left). FNA of a lymph node in

an 8 year old boy with infectious mononucleosis shows several atypical
lymphocytes (Diff-Quik stain, intermediate magnification). (Right) In situ
hybridization (ISH) for EBER in this specimen shows nuclear positivity in
several of the larger lymphocytes (intermediate magnification) (courtesy
of Dr. Sara Monaco, Department of Pathology, University of Pittsburgh
Medical Center, USA).
Fluorescent Stains 341
Fig. 14.11. ISH demonstrating Epstein-Barr virus in an oral smear from a

patient with hairy leukoplakia (high magnification) (courtesy of Dr. Shab-
num Meer, Division of Oral Pathology, University of the Witwatersrand,
Johannesburg).
Fluorescent Stains
●● Certain organisms when combined with fluorescent molecules
will fluoresce when viewed with a fluorescent light microscope.
This is based on the ability of some organisms to produce fluo-
rescent light after absorption of ultraviolet light. Fluorescent
molecules are called fluorophores or fluorochromes and include
green fluorescent protein and fluorescein. Several fluorescent
stains may be used simultaneously permitting information on
multiple parameters to be collected concurrently.
●● This technique is useful to rapidly identify various bacteria and
fungi that cause identical clinical conditions. Both P. jirovecii
and mycobacteria fluoresce when stained with a Papanicolaou
stain and viewed under a fluorescent microscope autofluoresce.
P. jirovecii cysts appear greenish yellow with irregular shapes
while mycobacteria appear as brilliant green bacilli.
Fig. 14.12. Fluorescence of Candida from an oral smear (high magnifica-

tion) (courtesy of Dr. Shabnum Meer, Division of Oral Pathology, Univer-
sity of the Witwatersrand, Johannesburg).
●● Fluorescent stains available for clinical use include the

acridine-orange stain, auramine-rhodamine stain, and Calcofluor
stains. The acridine-orange stain is used to detect thin bacte-
ria (e.g., Helicobacter) and fungi. The auramine-rhodamine
stain is used to detect acid-fast and partially acid-fast bacteria.
Calcofluor white stains yeast (e.g., Pneumocystis), fungi and
some parasitic organisms (e.g., Microsporidium, Acanthamoeba,
Naegleria, and Balamuthia spp.). Contaminants (e.g., cotton
fibers) may fluoresce strongly and must therefore be separated
from fungal hyphae.
●● The direct fluorescence monoclonal antibody stain (DFA) for
Pneumocystis appears to have higher diagnostic sensitivity than
silver stains like GMS (Figs. 14.12 and 14.13).
Flow Cytometry 343
Fig. 14.13. Autofluorescence of Mycobacterium tuberculosis in a lymph

node when viewed under a fluorescent microscope (Pap stain, high magni-
fication) (courtesy of Prof. Colleen Wright, Stellenbosch University, Cape
Town).
Flow Cytometry
●● Particles in a liquid sample are passed individually in front of
an intense light source. Light scatter and fluorescence of dif-
ferent wave lengths are measured. Multiple parameters can be
measured simultaneously. A single cell suspension is required
for flow cytometry, which makes cytologic specimens ideal.
●● Flow cytometry has numerous applications including lymphoma
and leukemia diagnosis, identifying and counting microbes
(such as bacteria, viruses, fungi, parasites), and evaluating the
host response to infection.
●● Flow cytometry is useful in managing HIV-infected patients by
measuring CD4 T-cell counts and CD4/CD8 ratios.
Serology
●● In terms of infectious disease, serology involves the use of blood
tests to detect the presence of antibodies against a microorgan-
ism. Some microorganisms (antigens) stimulate their human
host to produce antibodies. There are several serology tech-
niques that can be used depending on the antibodies being stud-
ied including enzyme-linked immunosorbent serologic assay
(ELISA), agglutination, precipitation, complement fixation, and
fluorescent antibodies.
●● Serology provides an indirect marker for current or past infec-
tion. IgM is useful as a measure of acute phase infection.
A fourfold or greater rise in antibody titer is indicative of acute
infection. IgG indicates past infection and determines if protec-
tive antibodies are present.
●● Serology is very useful in diagnosing atypical pneumonia,
syphilis, brucellosis, and many viral infections such as hepatitis,
HIV, and EBV if infectious mononucleosis is suspected.
Signal Amplification Assay

●● The nucleic acid hybridization assay is used to detect and quan-
tify RNA or DNA targets. The assay does not require preampli-
fication of the nucleic acid to be detected. Enzymes are used to
indicate the extent of hybridization, but unlike PCR are not used
to manipulate the nucleic acids. This technology facilitates high
throughput assays that can be used on a large number of samples
(e.g., HPV testing).
●● The Digene Hybrid Capture II (HC II) assay is a nucleic acid
hybridization microplate assay. It is an FDA-approved test used
to detect HPV DNA from both low- and high-risk HPV types.
There are several steps involved in the HC II assay (Fig. 14.14).
Polymerase Chain Reaction (PCR)

●● PCR is the amplification of a specific DNA or RNA sequence
whereby thousands or several millions of copies of that sequence
are generated. PCR is performed using cycles of repeated heat-
ing and cooling. At lower temperatures, double-stranded DNA
Polymerase Chain Reaction (PCR) 345
Fig. 14.14. Hybrid Capture II assay steps. (1) Target DNA is denatured.
(2) RNA-probes hybridize with target DNA. (3) The RNA-DNA hybrids
are captured onto the microplate well surface. (4) Amplification of hybrids
with multiple antibodies conjugated to an enzyme (alkaline phosphatase).
(5) The enzyme cleaves a chemiluminescent substrate, emitting light that
gets measured.
separates into two single-stranded DNA pieces. At medium tem-

peratures, short DNA fragments (primers) containing sequences
complementary to the target region pair up (anneal) with the sin-
gle-stranded DNA together with a DNA polymerase that starts
to copy the template. The template is then coupled to the primer,
producing a double-stranded DNA molecule. As the process is
repeated, more and more copies are exponentially produced.
The copies are referred to as amplicons. Very small quantities
can be amplified and analyzed, making cytology an appropriate
medium for PCR.
●● In the past, traditional PCR was time consuming. Today, rapid
cycle or real-time PCR methods are quicker and easier to per-
form. These are carried out in a closed system in which both
amplification and detection occur, reducing the potential for
contamination and false-positive results. Monoplex assays for
the detection of a single organism and multiplex assays, whereby
several organisms can be simultaneously detected are available.
●● PCR is useful for the diagnosis of organisms that are slow grow-
ing, fastidious or cannot be easily cultured (e.g., M. tuberculo-
sis, Legionella pneumophila, or P. jirovecii). PCR also permits
quantification of these organisms.
●● Problems related to PCR include false-positive (e.g., due to con-
tamination) and false-negative (e.g., technical failure) results.
●● Postamplification analysis consists of several different techniques

to obtain additional information that cannot be acquired from
the amplification technique alone and include melt curve analy-
sis, reverse hybridization, DNA sequencing, and microarray
technology.
●● Melt curve analysis. This assesses variants in DNA sequences
including mutations and single nucleotide polymorphisms. The
melting profile or temperature-dependent separation between
two DNA strands of a PCR product depends on its guanine-
cytosine content, length, sequence, and heterozygosity. This can
be measured with saturating dyes that fluoresce in the presence
of double-stranded DNA. This technique has been used to geno-
type various organisms (e.g., hepatitis viruses, mycobacteria,
salmonella species) and to investigate antimicrobial resistance.
●● Reverse hybridization. This technique is able to detect a vari-
ety of pathogens. The amplicon (PCR product) is labeled and
applied to a nitrocellulose membrane strip containing the rel-
evant probes. The amplicon will then hybridize to the com-
plementary species-specific probe, forming a banding pattern
on the nitrocellulose strip. Multiple species can be detected in
a single strip. This technique has been used to detect various
subtypes of mycobacteria, HIV, hepatitis C, and fungi.
●● DNA sequencing. This establishes the nucleic acid sequence of
the amplicon through Sanger sequencing (enzymatic procedure
to synthesize DNA chains of varying length to determine the
order of nucleotide bases) or pyrosequencing (determining the
sequence of nucleotide bases based on the incorporation of each
nucleotide as the strand of DNA is being synthesized). Once
the DNA sequence has been ascertained, it is compared to an
existing database to find a match. This technique has proved
very useful in identifying mycobacterial species, Nocardia,
and other actinomycetes, in addition to detecting antimicrobial
resistance.
●● Microarray technology. This technique permits one to study the
expression of thousands of genes simultaneously using hybridi-
zation of RNA or DNA that is placed in a specific order on a solid
surface and analyzed with the aid of a computer. This can be used
to rapidly identify pathogens, investigate antimicrobial resist-
ance, and determine host response to infection (Fig. 14.15).
Culture and Sensitivity 347
Fig. 14.15. Real-time PCR amplification curve for HHV-8 over 50 cycles.
The colored lines indicate different patients. Patients indicated with blue and
yellow lines are positive for HHV-8 DNA, while the samples from patients
indicated by red, purple and pink lines do not have HHV-8 DNA (courtesy
of Sharlene Naidoo, Department of Anatomical Pathology, University of
the Witwatersrand, Johannesburg).
Electron Microscopy (EM)

●● The role of electron microscopy (EM) has been greatly dimin-
ished in recent times with the development of new techniques
described above. This holds true for the diagnosis of infectious
diseases. However, the ultrastructural features of many patho-
gens have been well described and EM can certainly serve as a
useful adjuvant diagnostic modality when others are unavailable
or unsuccessful.
Culture and Sensitivity

●● Samples can be sent for culture and antimicrobial susceptibility
when an infectious process is suspected. Enriched media (e.g.,
blood agar, chocolate agar) are designed to support the growth
of most microorganisms. Selective media (e.g., MacConkey
agar) are designed to support the growth of only certain micro-
organisms and suppress the growth of others. Some organisms
Fig. 14.16. Culture plate of Nocardia spp. This photograph was taken
through a dissecting microscope and shows waxy and bumpy colonies on
culture (courtesy of Dr. Warren Lowman, Department of Microbiology,
University of the Witwatersrand, Johannesburg).
have very specific growth requirements (e.g., Legionella) and

will require more specialized media. Others may grow slowly
and thus may require an extended incubation (e.g., Bartonella).
Therefore, it is important to clearly communicate with the
microbiology laboratory the source of the specimen and sus-
pected pathogens.
●● Cytological findings at the time of specimen procurement (i.e.,
immediate evaluation) are able to help direct specific adjuvant
investigations (e.g., bacterial, fungal, or mycobacterial culture).
Material should be expelled into appropriate containers and/or
culture media. Alternatively, it can be washed into a sterile con-
tainer with saline to prevent desiccation of material. Aspiration
of pus may be related to an infection and hence such material
should be sent for culture. A dedicated pass often yields the best
results, but if unfeasible, needle rinses in culture media after
smears are made may be employed (Fig. 14.16).
Culture and Sensitivity 349
Acknowledgements Thanks to Carina Aitken, Head of the Special

Stains Section, Department of Anatomical Pathology, School of
Pathology, University of Witwatersrand, Johannesburg, SA, for
invaluable advice on special staining procedures and pitfalls.
Suggested Reading
Armbruster C, Pokieser L, Hassl A. Diagnosis of Pneumocystis carinii
pneumonia by bronchoalveolar lavage in AIDS patients. Comparison
of Diff-Quik, fungifluor stain, direct immunofluorescence test and
polymerase chain reaction. Acta Cytol. 1995;39:1089–93.
Atkins KA, Powers CN. The cytopathology of infectious diseases. Adv
Anat Pathol. 2002;9:52–64.
Bancroft J, Gamble M. Theory and practice of histological techniques. 6th
ed. London: Churchill Livingstone; 2008.
Bravo L, Procop G. Recent advances in diagnostic microbiology. Semin
Hematol. 2009;46:248–58.
Eyzaguirre E, Haque AK. Application of immunohistochemistry to infec-
tions. Arch Pathol Lab Med. 2008;132:424–31.
Hubbard RA. Human papillomavirus testing methods. Arch Pathol Lab
Med. 2003;127:940–5.
Lott RL. Fungi. In: Brown RW, editor. Histologic preparations: common
problems and their solutions. Chicago: CAP Press; 2009. p. 85–94.
Nuovo GJ. The surgical and cytopathology of viral infections: utility of
immunohistochemistry, in situ hybridization, and in situ polymerase
chain reaction amplification. Ann Diagn Pathol. 2006;10:117–31.
Oliveira A, French C. Application of fluorescence in situ hybridization in
cytopathology. A review. Acta Cytol. 2005;49:587–94.
Woods GL, Walker DH. Detection of infection or infectious agents by use
of cytologic and histologic stains. Clin Microbiol Rev. 1996;9:382–404.
hgbjkdfg
15
Mimics and Contaminants
Liron Pantanowitz1, Robert A. Goulart2,
and Rafael Martínez-Girón3
1
2
New England Pathology Associates, Mercy Medical Center, Sisters
of Providence Health System/Catholic Health East, 299 Carew Street,
Springfield, MA 01104, USA
3
CF Anatomía Patológica y Citología, Instituto de Piedras Blancas,
Piedras Blancas, Asturias 33450, Spain
Many potential artifacts and contaminants may be encountered

when examining cytology slides that could mimic true microor-
ganisms or cytopathic changes secondary to infection and thereby
lead to an erroneous diagnosis. An artifact is an undesired altera-
tion or artificial change in cytological material introduced by a
technique and/or technology, or unexpected material, e.g., talc.
Such modifications may occur at the time the sample is collected
or they may occur during or after laboratory processing of the
sample. The observation of bacteria in cytology specimens is a
common finding in certain specimen types, such as sputa, vaginal
smears, and voided urine. In most instances, they should not be
interpreted as a true infection, but rather as a contamination by the
saprophyte flora.
When artifacts and contaminants are encountered, their signifi-
cance and ways to avoid them should be determined. Critical issues
to resolve include whether the finding is an isolated (or random)
event, or if it signifies a more widespread (or systematic) problem
with specimen collection and/or processing. Both artifacts and con-
taminants may lead to problems with interpretation, creating confu-
sion with other structures of major relevance. The clinical context
of the patient (age, immune status, comorbid conditions, travel

352 15. Mimics and Contaminants
history, and immigration) is extremely important in these cases.

Intracellular organisms represent true infection, whereas gener-
ally the lack of an intimately associated inflammatory response,
necrosis, or cellular reactive changes in an immunocompetent
host favors a contaminant. Additional helpful indicators favoring
the presence of contamination rather than true infection include
(1) the presence of the structure on either the Pap or Romanowsky
stain but not both, (2) the structure lies on a different focal plane
than the inherent cellular material suggesting they were deposited
there at a different time, and (3) the structure is at the edge of the
glass slide.
In certain settings, these contaminants can be introduced by
patients into cytology samples, such as oral food particulate mate-
rial contaminating a respiratory specimen or fibers from a vaginal
pessary or sanitary pad seen in a cervicovaginal Pap test. An inter-
pretation of contamination should not be reported to avoid sub-
jecting the patient to unnecessary therapy, undue follow-up, and
perhaps further tests, whereas true infection should be diagnosed
and requires careful study of the patient’s immune status, prompt
investigation, and appropriate therapy.
There are a host of endogenous and exogenous structures
(Table 15.1) that may be mistaken for microorganisms (so-called
pseudomicrobes). These structures continue to pose diagnostic
problems for many cytologists due to a lack of familiarity or expe-
rience with them. This chapter covers several cytology artifacts
and contaminants that are likely to be seen in practice.
Mimics of Viral Infection

●● Koilocytes are squamous epithelial cells that exhibit struc-
tural changes following HPV infection. These cellular changes
include nuclear enlargement and irregularity, hyperchromasia,
and a perinuclear halo. When intracytoplasmic glycogen gets
dissolved, leaving a large clear space around the nucleus, these
cells in a Pap test may mimic koilocytes (Fig. 15.1). However,
such koilocyte-like cells lack all other morphological features of
dysplasia. Nonspecific perinuclear halos within superficial and
intermediate squamous cells in Pap tests may be associated with
Mimics of Viral Infection 353
Table 15.1. Endogenous and exogenous structures that mimic micro

organisms.
Endogenous structure Potential mimic
Blood Pneumocystis cast, Cryptococcus yeast
Platelets Extracellular parasites
Calcification Parasite ova and fungi
Psammoma body Parasite ova
Mucus Worms
Ciliocytophthoria Ciliated parasite and flagellated protozoa
Leisegang rings Parasitic ova and fungal yeast
Myospherulosis Endosporulating fungi
Tissue fiber (skeletal, elastic) Worms
Exogenous structure
Pollen Parasite ova
Dirt Bacteria
Vegetable matter Viral change and worms
Synthetic fibers and thread Worms
Dust and powder Parasite ova
Lubricant Pneumocystis cast
inflammatory conditions (e.g., Trichomonas infection), but can

also be an artifact due to slide preparation. These halos differ
from true koilocytes by their small size, indistinct edge, and the
symmetry of the halo about the nucleus.
●● Vegetable parenchymal cells may also resemble koilocytes. In
Pap tests, certain gels and pessaries containing excipient veg-
etable material are thought to be the source of such contami-
nants. Additionally, a number of unusual contaminants may be
detected in Pap tests due to women using environmental prod-
ucts, sometimes under the guidance of traditional healers. Labo-
ratory personnel should be aware of the local practices of their
communities and ethnic groups in order to be able to identify
these contaminants.
●● Cellular degeneration can be mistaken for viral changes including
Herpesvirus and Adenovirus, as well as the commonly seen
Polyomavirus effect in degenerated urothelial cells. Retroplasia,
characterized by the retraction of nuclear material, is a degen-
erative phenomenon that may be interpreted as viral infection,
especially CMV (Fig. 15.2) and Herpes virus infection.
Fig. 15.1. Pseudokoilocytes. Intermediate squamous cells from this Pap

test resemble koilocytes due to the loss of perinuclear intracytoplasmic
glycogen. Note that their nuclei do not have dysplastic features character-
istic of true koilocytes, but resemble those of nearby intermediate squa-
mous cells (Pap stain, high magnification).
●● Reactive-atypical endocervical cells may resemble the cytologic

changes associated with Herpes Simplex Virus (HSV) infection
(Fig. 15.3). This is a known potential pitfall in endocervical
brush specimens. Despite the presence of multinucleation and
nuclear molding in reactive endocervical cells, the chromatin
pattern, presence of macronucleoli, and absence of intranuclear
inclusions are important to establish the appropriate differential
diagnosis.
Ancillary Studies
●● Immunocytochemistry for specific viruses.
Fig. 15.2. Retroplasia. These bronchial epithelial cells on a sputum
smear show degenerative changes. Note the chromatin condensation
(retroplasia) mimicking intranuclear inclusions similar to CMV (Pap
Fig. 15.3. Pseudo-herpes on a Pap test. Reactive endocervical cells, often

with multinucleation, are shown mimicking herpetic infection on a con-
ventional smear (left) and a ThinPrep (right) Pap test. Note the sheet of
normal endocervical cells present in the top of the upper left image (Pap
stains, left intermediate magnification, right high magnification).
Mimics of Bacterial Infection

●● Normal bacterial flora is a common finding in vaginal specimens
(lactobacilli), oropharyngeal contamination in sputa, and voided
urine. These should not be interpreted as a true infection, but
rather as a contamination by the saprophyte flora (Fig. 15.4).
●● If a fluid is placed in an unsterile container, has a long time delay
in reaching the laboratory, or is not refrigerated, overgrowth of
contaminating bacteria may be marked.
Fig. 15.4. Normal oral flora. (Upper left, high magnification) Sarcina
forms on a sputum smear, illustrating their characteristic appearance in
tetrads (buckets of eight elements). This type of bacteria is frequently
observed as a commensal flora in the mouth (Pap stain). (Bottom left, high
magnification) Leptotrichia buccalis present as a contaminant on a spu-
tum smear (Pap stain). (Upper right, high magnification) Actinomyces-
like organisms contained within a sputum smear. Their presence indicates
oral contamination and not a true infection (Pap stain). (Bottom right,
intermediate magnification) Oropharyngeal contamination composed of
anucleate squames and filamentous bacteria present within the cell block
of a bronchoalveolar lavage specimen (H&E stain).
Mimics of Fungal Infection 357
●● Bacteria may be introduced onto slides by bacterial growth

contaminating stain solutions.
●● Dirt, granular debris, precipitate material, pencil graphite, and
silver nitrate crystal contamination in Pap tests may resemble
clumps of bacteria. If these contaminants are not part of the
specimen, they will be slightly out of the plane of focus with the
routine cellular material.
●● In vitreous fluid, small fusiform melanosomes released from
degenerating choroid tissue may resemble bacteria. These rods
may also be phagocytosed by macrophages.
Ancillary Studies
●● Gram stain
●● Bacterial culture
Mimics of Fungal Infection

●● Various fungi (e.g., Alternaria, Aspergillus, Cladosporium,
Fusarium, Penicillium spp., etc.) are ubiquitous in the environ-
ment (Table 15.2) and thus may easily be introduced into cytol-
ogy samples or make their way onto glass slides (Figs. 15.5 and
15.6) from contamination of collection materials (e.g., spatu-
las), laboratory equipment (e.g., stain solutions and dishes),
and cell blocks. One may find the entire conidiophore (fruiting
body composed of specialized fungal hyphae that produce
conidia) or other fungal elements such as a swollen vesicle,
phialides (dilated portion of the conidiophore), and/or isolated
conidia (spores). Any of these fungi, however, may become
opportunistic pathogens in the immunosuppressed host. Numer-
ous spores arranged in chains, sometimes characteristic of
Aspergillus and Penicillium, can resemble coccoid bacteria or
erythrocytes.
●● In respiratory cytology samples, Candida spp. elements
obtained from the mouth frequently represent a “contaminant”
of the respiratory specimen. This is often the case in immuno-
suppressed patients, such as individuals with AIDS who have
oral thrush.
Table 15.2. Comparison of different airborne fungal contaminants.

Fungus Fungal elements
Alternaria Club-shaped septate conidia
Aspergillus Fruiting body and septate hyphae
Cladosporium Dark conidia with branching chains
Fusarium Sickle-shaped septate conidia
Penicillium Fruiting structures and septate hyphae
Fig. 15.5. Alternaria spp. (high magnification images). (Upper left)

Sputum smear containing a “racket-shaped” macroconidia (Pap stain).
(Bottom left) Alternaria tenuissima in a cervicovaginal smear. Several
branching hyphae are originating from a macroconidia placed at the left of
the image (Pap stain). (Upper right) Sputum smear showing macroconidia
with four attached septated hyphae (Pap stain). (Bottom right) Brown
club-shaped septate macroconidia seen in fungal culture (Lactol Phenol
Cotton Blue stain).
●● Erythrocytes, particularly degenerating and “ghost” red blood

cells, may mimic yeast (Fig. 15.7). Table 15.3 illustrates a
number of the morphological features that can be used to
differentiate red blood cells from true yeast. Foamy alveolar
Fig. 15.6. Fungal contaminants. (Upper left) Cladosporium spp. found

on a cervicovaginal smear. At the left of the image, we can observe the
typical spores (ovoid in shape and forming short chains), and at the right,
septate and branched hyphae (Pap stain, high magnification). (Bottom
left) Penicillium spp. present within a sputum smear. These species, the
most abundant genus of fungi in soils and food, are recognized by their
brush-like spore-bearing structures. Branching is an important feature
for identifying Penicillium spp. (Pap stain, high magnification). (Upper
middle) Geotrichum present within a sputum smear. This fungus appears
as long segmented hyphae and rectangular arthroconidia with squared
ends. Geotrichum is a ubiquitous saprophyte found in soil, decomposing
organic matter, and contaminated food. It is also a transient commensal of
the oropharynx, being frequently isolated from sputum and stool samples
of normal persons (Pap stain, high magnification). (Bottom middle) Cer-
vicovaginal smear with the presence of a dense Chaetomium spp. fungal
mass-like ball surrounded by numerous filaments corresponding to long
hyphae (Pap stain, intermediate magnification). (Upper right) Fruiting
bodies of Aspergillus spp. These structures have swollen vesicles at the
end of a conidiophore. Hyphal segments are also observed (Pap stain, high
magnification). (Bottom right) Aspergillus-like artifact. This is really a
cotton fiber with a cannonball of leukocytes that resembles a fruiting body
in a Pap smear (Pap stain, high magnification).
casts seen with Pneumocystis infection in the lung are better

circumscribed than lysed red blood cells. True Pneumocystis
casts may also be mimicked by debris, lubricant, amyloid, and
alveolar proteinosis.
Fig. 15.7. Red blood cell fungal mimics. (Upper left) Acetic acid effect is
shown on erythrocytes in a Pap smear. Due to their decoloration, these red
blood cells may be misinterpreted as fungal yeast. Their size, relatively
uniform morphology, and absence of both budding and clear halos are
important keys to the differential diagnosis (Pap stain, high magnifica-
tion). (Bottom left) Erythrocytes contained within a bronchoalveolar lavage
(BAL) smear mimic Pneumocystis microorganisms. Red blood cells have
irregularities and thickenings in their outlines and condensation of content
in the center (Pap stain, high magnification). (Upper right) Degenerated
erythrocytes on a cervicovaginal smear, likely due to ethanol. Because of
their appearance, they could be confused with fungal yeasts (Pap stain,
high magnification). (Bottom right) Granular bloody cast seen in a BAL
specimen resembling an alveolar cast of Pneumocystis infection. Unlike a
true cast, this blood aggregate has irregular edges (Pap stain, intermediate
magnification).
●● Spermatozoa may mimic yeast, particularly when only their

head is visible in stained material.
●● Many vegetable or synthetic fibers as well as contaminating
threads on cytology slides can resemble portions of fungal
hyphae, especially when these are highlighted with a GMS stain
(Fig. 15.8).
Table 15.3. Cytomorphological features comparing common yeast to

erythrocytes.
Structure Yeast Erythrocyte
Size (mm) 3–6 5–7
Shape Round-ovoid Round
Color Variable Red-orange
Budding Yes No
Clear halos Yes No
Appendages No No
Fig. 15.8. Fungal mimics. Multiple structures are shown that resemble
fungal hyphae, as seen within several direct smear preparations (Pap and
Diff-Quik stains, high magnification).
●● Macrophages containing phagocytosed material within intra-

cytoplasmic vacuoles may be mistaken for organisms such as
Histoplasma capsulatum.
●● Talc granules from talcum powder can mimic fungal yeast
(Fig. 15.9). Talc is a mineral composed of hydrated magnesium
silicate. The granules form crystalloid, transparent, and polygonal
Fig. 15.9. Talc. (Left) Talc crystals on a cervicovaginal smear appear as

crystalloid, transparent, and polygonal structures with a dark striation in
the middle (Pap stain, high magnification). (Right) Talc crystals within a
sputum smear (Pap stain, high magnification).
structures with a dark striation in the middle. Using polarized

light, the typical “Maltese cross” image will appear.
●● Pollen grains may mimic parasite ova (Fig. 15.10). They can
be differentiated by their larger size, thick cell wall, and refrac-
tile appearance. Sporangia are plant, fungal, or structures from
algae containing spores that may be encountered in respiratory
cytopathology. Some sporangium-like spherules may mimic
Coccidiodes immitis sporangia containing endospores.
●● Calcification may resemble fungal yeast when it is fragmented
or hyphae when it is linear and branching (Fig. 15.11).
●● Myospherulosis is the alteration of red blood cells, following
exposure to fats or fat products (e.g., petrolatum, lanolin, human
fat), into many 4–7 mm smooth, refractile or oily, spherules that
are typically enclosed in a sac-like structure (parent body). The
spherules can also be dispersed singly. This can occur after
hemostatic packing (e.g., of the nasal cavity or paranasal sinuses
with petrolatum-based ointment and gauze), via intramuscular
injection with ointments, or from endogenous lipid breakdown
(postsurgical or blunt trauma). Myospherulosis is not an uncom-
mon finding in FNA of fat-containing sites like the breast and
subcutaneous tissue, and may be seen accompanying fat necro-
sis. Altered red blood cells do not appear to be lysed following
exposure to hemolytic solutions. These structures are readily
Fig. 15.10. Pollen grains (high magnification images). (Upper left) Pollen
grains belonging to the Betulaceae family seen within a sputum smear. In
these structures, a refractile capsule and three surface apertures (pores) are
observed (Pap stain). (Bottom left) Pollen grain belonging to the Pinaceae
family present within a sputum smear. Because their airborne sacs are
broken, the undulations on the wrinkled surface may mimic an Ascaris
lumbricoides egg (Pap stain). (Upper right) Pollen grains belonging to
the Liliaceae family detected on a sputum smear. The grains are large
(about 300 × 150 mm), ovoid in shape, with refractile capsules and notable
folds on the surface (Pap stain). (Bottom right) Pollen grains belonging to
the Caryophyllaceae family present within a sputum smear. Due to their
round shape (approximately 70 mm in diameter) and evident capsule, these
structures may be mistaken for Toxocara eggs (Pap stain).
seen with a Pap stain, but fail to stain with GMS and PAS stains.
They may resemble endosporulating fungi like coccidiomycosis
and rhinosporidiosis, as well as other sporangia.
Ancillary Studies
●● Special stains (GMS, PAS) for fungi
Fig. 15.11. Calcification mimicking fungal (left) hyphae and (right) yeast
(H&E stain, intermediate magnification).
Mimics of Parasitic Infection

●● Parasite worms can be mimicked (Fig. 15.12) by human tissue
fibers (e.g., skeletal muscle or elastic fibers), suture material,
strands of mucus (e.g., Curschmann spirals), vegetable matter
(e.g., plant hairs) as well as contaminating exogenous synthetic
fibers and plant threads (cotton, cellulose, rayon, etc.) or fer-
ruginous bodies (seen mainly in patients with pneumoconiosis).
The presence of unusual shapes (e.g., sharp kinks) and lack of
both external (e.g., mouth, hooks, etc.) and internal (e.g., diges-
tive or reproductive tract) recognizable anatomical structures
are often essential to differentiate artifacts from real worms.
Curschmann spirals are formed from inspissated mucus and can
be found in cervical Pap tests, respiratory tract specimens, and
even fluids which contain mucus. Skeletal muscle fibers typi-
cally have nuclei distributed longitudinally along the periphery
and have cross striations. Their presence in respiratory speci-
mens may be derived from food contamination or aspiration.
Mimics of Parasitic Infection 365
Fig. 15.12. Worm mimics. (Upper left) Synthetic fiber observed on a

sputum smear. In spite of the characteristic spiral arrangement mimicking
a filariform larva of Strongyloides stercoralis, the presence of numerous
fine dots covering the entire surface and the two ends terminating abruptly
are very characteristic. Moreover, note the absence of internal anatomical
structures (Pap stain, high magnification). (Bottom left) Multiple synthetic
fibers present in a CSF liquid based slide (Pap stain, intermediate magnifi-
cation). (Upper right) Striated skeletal muscle fiber in a sputum smear. In
spite of its spiral arrangement, the right end is interrupted sharply, there is
an absence of internal structure, and the large diameter (about 60–100 mm
in width) is an important key to not confuse this with a true parasite (Pap
stain, high magnification). (Bottom right) Curschmann spiral embedded
in mucus in a respiratory sample (Pap stain, high magnification).
Synthetic fibers covered in dots are indicative of rayon, whereas

those with a series of lines forming a fringe along the entire
length are characteristic of cotton. Because several of these arti-
facts are refractile and may be birefringent, the utilization of
polarized light is a useful ancillary technique to recognize them.
Sutures or retained foreign material (e.g., fibers from retained
surgical gauze or sponges) are typically accompanied by either
acute inflammation (if recently introduced into the patient) or
foreign-body type granulomatous inflammation (if the surgical
procedure was performed in the patient’s remote past).
●● Parasite ova can be mimicked by psammoma bodies, crystals in
urine sediment, corpora amylacea, bile microspheroliths, pollen,
vegetable cells, dust, and even certain powders contaminating
slides. In urine, the presence of a lateral spine, miracidium inside
eggs, and background eosinophilia can help differentiate urine
crystals (especially “lemon-like” uric acid crystals) from true
Schistosoma haematobium eggs.
●● Cellular degeneration may mimic certain parasites (Fig. 15.13).
In cervicovaginal Pap tests, the presence of bare nuclei among
cellular inflammatory debris in cases with atrophic change and
cytolysis could be misinterpreted as trichomoniasis. Degenera-
tive changes in leukocytes may also mimic the presence of tri-
chomonas on a cervicovaginal smear. Compared to bare nuclei
of parabasal cells and degenerated cells, trophozoites of Tri-
chomonas vaginalis are pyriform in shape, measure 7–30 mm in
length × 6–15 mm in width, have four anteriorly directed flagella
and one directed posteriorly, a nucleus situated in the anterior
portion of the organism, and cytoplasmic granules. Flagella may
be hard to visualize.
●● Ciliocytophthoria are degenerated anucleate, apical remnants of
ciliated epithelial cells (Fig. 15.14) that may be mistaken for
the oval ciliated parasite Balantidium coli or multi-flagellated
protozoa (Hypermastigida). Detached ciliary tufts may be seen
in respiratory specimens associated with viral infection (par-
ticularly adenovirus), Pap tests, or peritoneal fluid specimens
where they are associated with physiologic shedding from the
female genital tract, and as contaminants in amniotic fluid
during amniocentesis. Motile forms may be observed in fresh
(wet) nasopharyngeal and peritoneal specimens. In fresh speci-
mens, cellular tufts may retain cilial motility for several hours.
Mimics of Parasitic Infection 367
Fig. 15.13. Degenerative cellular changes (high magnification images).

(Upper left) Atrophic changes in a conventional cervicovaginal smear.
Due to the background with abundant cellular debris, bare nuclei, and
cellular necrosis, this pattern could be misinterpreted as trichomoniasis
(Pap stain). (Bottom left) Degenerative changes in leukocytes, mimick-
ing the presence of Trichomonas on a conventional cervicovaginal smear.
Numerous spermatozoa are also observed (Pap stain). (Upper right) Cyto-
lytic changes are shown on a conventional cervicovaginal smear. This
pattern, with the presence of bare nuclei and cellular debris, could also
be misinterpreted as trichomoniasis. Numerous lactobacilli are also seen
(Pap stain). (Bottom right) Neutrophils with fragmented nuclei are present
within a conventional cervicovaginal smear. These elements may be mis-
taken for microorganisms, such as fungal yeast (Pap stain).
I nfections due to B. coli are rare and mainly involve the large
intestine. B. coli are much larger (40–100 mm) than ciliocytoph-
thoria (10–12 mm). Ciliocytophthoria usually demonstrate cilia
resting on a terminal bar predominantly along one edge whereas
B. coli are uniformly covered with cilia. Also, ciliocytophthoria
Fig. 15.14. Ciliocytophthoria. Multiple anucleate, apical remnants of

ciliated epithelial cells are shown scattered among a few inflammatory
cells in this Pap test slide (Pap stain, high magnification).
are anucleate compared to B. coli which contain a macronu-

cleus. Multi-flagellated protozoa show irregular insertion of
flagella, absence of a terminal bar, and prominent nuclear halos.
One may also find detached single cilia in brochoalveolar lav-
age specimens that mimic bacilliform structures.
●● Leisegang rings (or bodies) are nonpolarizable laminated ring-
like structures (Fig. 15.15) occasionally found in benign cysts
and abscesses. They are of variable size (3–800 mm), usually
have a double-layer outer wall, faint radial striations, and an
amorphous central core. They may be confused with parasites
(especially eggs), but also with algae and psammoma bodies.
Unlike ova, they lack flattening on one side or at the poles and
show marked variation in size. They are easily observed with
Pap (green color), H&E (pink), Diff-Quik (purple) stains, and
a few other (Masson’s trichrome, acid-fast, Gram) stains which
accentuate their concentrically laminated morphology. They do
not stain with GMS, PAS, or von Kossa stains.
Plant Contaminants and Mimics 369
Fig. 15.15. Leisegang rings. These cell block specimens prepared from
fine needle aspirates of hemorrhagic cysts show laminated ring-like struc-
tures. (Left) The bodies present are of variable size and shape. Some rings
contain a distinct double-layer outer wall (H&E stain, intermediate mag-
nification). (Right) In these two darker colored Leisegang rings, one can
see faint radial striations and an amorphous central nidus (H&E stain, high
magnification).
Ancillary Studies
●● Light polarization or specialized illumination (e.g., Nomarski
technique) used to enhance the contrast in unstained, transpar-
ent samples.
●● Serology for parasite exposure and eosinophilia
●● Von Kossa stain for calcification
Plant Contaminants and Mimics

●● Slides may contain plant tissue cells (sclerenchyma) including
fibers and sclereids (Fig. 15.16). Each has hard cell walls. Fib-
ers are generally long and slender whereas sclereids are shorter
and more variable in shape. An asterosclereid is a type of scle-
reid cell that tends to be radially branched. Plant cells have been
Fig. 15.16. Asterosclereids. (Upper left) A fragment of epidermal plant

tissue is contained within a sputum smear. Note at the bottom of the image
the presence of two squamous cells (Pap stain, intermediate magnification).
(Bottom left) Plant epidermal cells present in a cervicovaginal smear. They
have characteristic undulating thick walls (Pap stain, high magnification).
(Right) Single asterosclereid cells are shown with Diff-Quik (Upper right,
high magnification) and Pap (Bottom right, high magnification) stains.
reported to resemble koilocytes and tumor cells in cytology

specimens.
●● Trichomes (meaning “growth of hair”) are the fine appendages
(e.g., hairs) found on some plants (Fig. 15.17). These plant hairs
may have blunt or tapering ends and an internal refractile core.
●● Pollen grains come in a wide variety of shapes (most often
spherical), sizes (6–100 mm), and surface markings character-
istic of their plant species (Fig. 15.10). A mature pollen grain
has a double wall that includes a thin delicate inner wall (called
the intine) and a tough outer cuticle (called the exine). Unlike
parasite ova, an internal structure is not visualized. They usually
do not show birefringence under polarized light compared to
crystals. Pollen can mimic yeast, parasitic ova, and psammoma-
tous calcification.
Plant Contaminants and Mimics 371
Fig. 15.17. Trichomes. (Upper left) Epidermal plant tissue observed on

a sputum smear showing numerous hairs (trichomes) and pores (stomata)
(Pap stain, intermediate magnification). (Bottom left) Single trichome
is shown in a Pap test specimen mimicking an Enterobius vermicularis
worm (Pap stain, high magnification). (Upper right) Trichome seen on
a cervicovaginal smear. Note the thorny appearance and thick walls (Pap
stain, high magnification). (Bottom right) Trichomes shown on a sputum
smear. In spite of its branching appearance, the presence of thick walls, no
budding, and lack of septae are important features that help to differentiate
these structures from true fungal hyphae (Pap stain, high magnification).
●● Sporangia are plant, fungal, or algal structures containing spores.

Sporangium-like structures may be encountered that mimic true
sporangia. The absence of free endospores around these struc-
tures and absence of a well-defined cell wall favor an artifact
mimicking sporangia.
●● Algae are plant-like organisms (autotrophic protists) that grow
in water. Their presence on cytology slides as single structures
or as colonies (Fig. 15.18) is mainly due to tap water con-
tamination from using aqueous solutions or washing slides in
water. They can be unicellular or multicellular and may assume
different and peculiar morphologies (e.g., filamentous, spheroid,

crystalloid, etc.). They include diatoms (phytoplankton) and

Fig. 15.18. Algae (high magnification images). (Upper left) Diatom frus-
tule (Navicula spp.) present within a sputum smear. Note the characteris-
tic thick silicified cell wall, elongate shape, and presence of transversal
striations in this diatom (Pap stain). (Bottom left) The freshwater red algae
belonging to Rhodophyta was identified in this Pap smear. The round
forms are arranged as beads on a necklace (Pap stain). (Upper right) Spu-
tum smear in which a sphere-like structure containing numerous round
cells was identified, compatible with Eudorina spp. (Pap stain). This
could be mistaken for adenocarcinoma. (Bottom right) In this cervicovagi-
nal smear, there is an unbranched filament (Ulothrix spp.) with identical
C-shaped chloroplasts and thick cellular walls (Pap stain).
dinoflagellates (flagellated plankton). Diatoms range in size

from 2 to 200 mm and are contained within a unique hard
silicate crystalloid cell wall (shell). Their morphology varies.
While most diatoms are circular in shape, some may be ellipti-
cal, triangular, or even square. Some of these plant cells con-
sist of filaments (e.g., Ulothrix). Certain filamentous organisms
enclosed in a gelatinous sheath (e.g., Oscillatoria spp.) may
mimic parasite worms. Most dinoflagellates are unicellular forms
with two flagella. These flagellated structures may be confused
Animal Contaminants and Mimics 373
with pathogens (e.g., fungi, parasites) or other elements such

as fibers, pollen grains, crystals, fecal contamination, and even
malignant cells. Volvocales algae (also called Chlamydomon-
adales) can form spherical (moruliform) colonies embedded in
a clear matrix that may resemble adenocarcinoma. Freshwater
red algae (Rhodophyta) characteristically form round elements
arranged as beads on a necklace (Fig. 15.18). These “strings
of pearls” have been interpreted by some authors to represent
blue bobs in postmenopausal atrophy on Pap tests. In forensic
pathology, the presence of diatoms in certain organs (e.g., lung,
bone marrow, etc.) provides complementary evidence in the
diagnosis of death by drowning.
Ancillary Studies
●● Expert consultation (e.g., microbiologist, botanist)
Animal Contaminants and Mimics

●● Entire insects or parts (head, thorax, wing, jointed leg, antennae)
of an insect may sometimes be trapped under a coverslip of a
glass slide (Fig. 15.19).
●● Carpet beetle hairs are infrequent contaminants (Fig. 15.20).
Carpet beetles are one of the most common insects found in
homes. Adult carpet beetles are oval and approximately 1/8 in.
long. Their larvae are covered with short hairs or bristles.
●● Dust mites occasionally can be found in cytology specimens
(Fig. 15.21). The average dust mite measures 0.4 mm in length
by 0.25 mm in width. Their body is somewhat rectangular shape
and like all acari they have eight legs.
●● Several small invertebrates (zooplankton) including aquatic crus-
taceans (water fleas), rotifers (commonly called wheel animals),
and ciliates (e.g., Vorticella) may be identified as contaminants.
Daphnia (freshwater water fleas) is the most commonly known
genus. Their body is covered by a carapace and they have 5 or 6
pairs of legs and prominent antennae. They may have elaborate
appendages and filaments (Fig. 15.22) that facilitate their flota-
tion and food capture. Rotifers are approximately 0.1–0.5 mm
Fig. 15.19. Insects (intermediate magnification images). (Upper left)

In this image from a voided urine specimen, we can observe the ventral
aspect of an entire arthropod. It is possible to identify two antennae and
three pairs of segmented legs. The insect is partially covered by a coat of
bacteria (Pap stain). (Bottom left) In this sputum smear, there is a fragment
of an arthropod leg mimicking a Taenia-like organism (Pap stain). (Upper
right) Sputum smear showing a structure formed by a mixture of mucus
and bacteria that may be misinterpreted as a mite (Pap stain). (Bottom
right) Wood fragment (cellulose fibers) contained within a cervicovaginal
smear with an arthropod-like appearance (Pap stain).
long, contain three body sections (head, thorax, foot), have a

well-developed cuticle that may bear spines or ridges, exhibit a
variety of different shapes (typically somewhat cylindrical), and
bear a characteristic ciliated structure (called the corona) on their
head. Vorticella are ciliated protozoa that mainly live in fresh-
water ponds and streams. Each of these cells contains a nucleus
(with or without vacuoles) and a characteristic long stalk.
Ancillary Studies
●● Expert consultation (e.g., microbiologist, zoologist)
Fig. 15.20. Carpet beetle. (Left) Bottom portion of a carpet beetle larva
covered with many hairy bristles (low magnification). (Right) A carpet
beetle hair contaminant present on a cervicovaginal Pap test (Pap stain,
Fig. 15.21. Dust mites (intermediate magnification images). (Left) This

dust mite specimen was observed as a contaminant within a breast FNA
cell block specimen. Note the four pairs of legs (H&E stain). (Right) Dust
mite found on a sputum smear (Pap stain).
Fig. 15.22. Water contaminant on a sputum smear. This image shows part
of an aquatic insect (Daphnia spp.) with numerous filtering filaments (Pap
Suggested Reading
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Index
A Amebae (sarcodina), 71
Abscess, 132 Anal disease, 303–304
brain, 219–221 Anal Pap test, 176, 177
breast, 259 Ancillary investigations
liver, 176–179 bacterial stains
Acid-fast stains, for mycobacteria, acid-fast stains,
327, 328 mycobacteria, 327
Actinomyces, 51, 53 Gram stain, 324–325
gynecological infections Helicobacter pylori, 325–326
ancillary tests, 106 Warthin–Starry stain,
clinical features, 104, 105 326–327
cytomorphologic features, 105 cell blocks, 323
diagnosis, 105 culture and sensitivity, 347–348
microbiology, 104 electron microscopy (EM), 347
pulmonary infections flow cytometry, 343
ancillary studies, 133 fluorescent stains, 341–343
clinical features, 132 fungal stains
cytomorphologic features, characteristics, 328, 330
132–133 Fontana-Masson stain, 331
differential diagnosis, 133 immunocytochemistry
microbiology, 132 antibodies, 335–337
Adenovirus, 44 Aspergillus, 335, 338
pulmonary infections Pap test, 335, 339
ancillary studies, 128 in situ hybridization (ISH)
clinical features, 127 advantages, 335
cytomorphologic features, cervix condyloma, 339, 340
127–128 Epstein–Barr virus, 339, 341
differential diagnosis, 128 infectious mononucleosis.,
pneumonia, 126, 128 339, 340
urinary tract infections, 192 polymerase chain reaction (PCR)
AIDS-related lymphomas (ARL), 309 amplicons, 345
Algae, 82–83 DNA sequencing and melt
Allergic mucin, 15–16 curve analysis, 346

Essentials in Cytopathology 17, DOI 10.1007/978-1-4614-0242-8,
380 Index
Ancillary investigations (cont.) B

microarray technology, Bacillary angiomatosis, 274–276
346, 347 Bacilliary peliosis, 252
postamplification Bacteria
analysis and reverse acid-fast stains, mycobacteria
hybridization, 346 chemical property, 327, 328
uses, 345 modified fite stain, 327, 329
Rickettsial stains, 331–332 Ziehl–Neelsen stain, 327, 329
routine cytology stains acute meningitis
H&E stain, 323 ancillary studies, 212
Pap stain, 322 clinical and cytomorphologic
Romanowsky stains, 322 features, 210
Toluidine blue, 323 differential diagnosis, 211
serology, 344 microbiology, 209
signal amplification anerobic bacteria, 47
assay, 344, 345 Chlamydia, 51–54
stains, parasites, 332 conjunctivitis, 296
viral stains, 332–334 cystitis
wet mount preparation, 324 acute, 190
Angiostrongyliasis, 229–230 ancillary studies, 190
Animal contaminants and mimics cytomorphologic features, 189
carpet beetles, 373, 375 differential diagnosis, 190
dust mites, 373, 375 follicular, 192
insects, 373, 374 in urine, 191
invertebrates, 373 eye infection, 296
Antiretroviral therapy (ART), 302 filamentous bacteria, 51–53
Apicomplexa, 74–76 Gram-positive and Gram-negative,
ARL. See AIDS-related 47–49
lymphomas (ARL) Gram stain, 324–325
Arthritis, 273–274 gynecological infections
Aseptic meningitis. See Viruses, Actinomyces, 104–106
meningitis bacterial vaginosis
Aspergillosis (BV), 101–103
ancillary studies, 148–149 Chlamydia trachomatis,
clinical features, 147 108–110
cytomorphologic features, granuloma venereum,
147–148 106, 107
differential diagnosis, 148 Neisseria gonorrheae,
microbiology, 147 103–104
paragonimus eggs, 149 tuberculosis (TB), 106–108
in ThinPrep preparation, 148 Helicobacter pylori, stains
toxoplasmosis, in BAL for, 325–326
specimen, 156 mycobacteria, 48–50
Aspergillus, 58–60, 62 osteomyelitis, 273
crystal formation in, 34 pulmonary infections
Asteroid bodies. See Splendore- Actinomyces, 132–133
Hoeppli phenomenon Legionella, 137–138
Index 381
Nocardia, 133–134 Botryomycosis, 271

tuberculosis (TB), 135–137 Brain abscess, 219–221
rhinosinusitis, 291 Breast abscess, 259
Warthin–Starry stain, 326–327 Breast infections
Bacterial vaginosis (BV) acute mastitis and abscess
ancillary tests, 102–103 ancillary studies, 261
clinical features, 102 clinical features and
cytomorphologic features, 102 definition, 259
diagnosis, 102 cytomorphologic features,
vaginal flora, shift in, 101 subareolar abscess, 259
Bacteriology, 7, 8 chronic and granulomatous
Bartonella henselae, 326 mastitis, 261–262
bone and joint infections, 274 inflammatory lesions, 257, 258
lymph node infections, 234–236 lymphoma, 259
spleen infections, 252 parasitic, 262
Bartonella quintana, 326 Staphylococcus aureus, 257
Benign lymphoepithelial cysts Bronchoalveolar (BAL) specimen
(BLECs), 306–308 candidiasis in, 139
Bilharzia. See Schistosomiasis CMV and Pneumocystis
BK virus (BKV), 44–45 jirovecii, 127
ancillary studies, 197 herpes simplex virus, 124
clinical features, 194–195 Strongyloides stercoralis, 153
cytomorphologic features, toxoplasmosis in, 156
195–197 BV. See Bacterial vaginosis (BV)
decoy cells, 194, 195
differential diagnosis, 197
microbiology, 193–194 C
polyoma virus infection, 196 Calcium oxalate crystals, 33, 34
Bladder schistosomiasis, 200 Candida, 55–57, 62
Blastomyces, 61, 63, 66 Candida glabrata, 111, 112
Blastomyces dermatitidis, 219 cystitis, 199
Blastomycosis, 142 esophagitis, 163
ancillary studies, 221 in gynecological infections
clinical features, 219 ancillary tests, 112
cytomorphologic features, 220 clinical features, 110
differential diagnosis, 220 cytolomorphogic features,
BLECs. See Benign lymphoepithelial diagnosis, 111–112
cysts (BLECs) microbiology, 110
Bone and joint infections oropharyngeal infections
arthritis, 273–274 Candida albicans, 289
bacillary angiomatosis, 274–276 Candida glabrata, 290
bacterial osteomyelitis, 273 Candidiasis
Cryptococcus, 273 oral, 289–291, 305
synovial fluid characteristics, in pulmonary infections
274, 275 ancillary studies, 140
382 Index
Candidiasis (cont.) mollaret meningitis

in BAL specimen, 139 ancillary studies, 216
clinical features, 139 clinical and cytomorphologic
cytomorphologic features, 139 features, 215
differential diagnosis, 140 differential diagnosis, 216
microbiology, 138–139 microbiology, 214
Cat scratch lymphadenitis, 234–236 monocytic pleocytosis, 206
Cavity formation, 121, 135, neurocysticercosis, 227
147, 157 neurosyphilis, 223–225
Cell blocks, 323 neutrophilic pleocytosis, 206
Central nervous system (CNS) primary amebic meningoen-
infections, 11 cephalitis, 228
acute bacterial meningitis shunt infections, 222–223
ancillary studies, 212 toxoplasmosis, 225–227
clinical and cytomorphologic tuberculous meningitis, 216–217
features, 210 viral meningitis
differential diagnosis, 211 ancillary studies, 213–214
microbiology, 209 clinical features, 212
angiostrongyliasis, 229–230 cytomorphologic features,
bacterial infections, 205, 206 212–213
blastomycosis differential diagnosis, 213
ancillary studies, 221 microbiology, 212
clinical features, 219 Cervical carcinoma, 92
cytomorphologic features, 220 Cervicofacial actinomycosis
differential diagnosis, 220 Actinomyces israelii, 287
microbiology, 219 oral actinomyces flora., 287, 288
brain abscess, 219–222 Cervicovaginal disease, 303–304
cerebrospinal fluid pleocytosis, Cestodes (tapeworms), 78–79
205, 207 Charcot-Leyden crystals, 16, 33
cryptococcal meningitis Chlamydia
ancillary studies, 219 Chlamydia pneumonia, 52
clinical features, 218 Chlamydia psittaci, 53
cytomorphologic features, Chlamydia trachomatis, 53, 236
218–219 ancillary tests, 109–110
differential diagnosis, 219 clinical features, 109
microbiology, 217 cytomorphologic features, 109
CSF parameters, 206, 208 diagnosis, 109
disease, in immunosuppressed microbiology, 108
host forms, 51
mass lesions, 312 Chlamydial eye infection, 296
meningitis, 310–311 Chlamydomonadales, 373
progressive multifocal Chromomycosis, 270–271
leukoencephalopathy, Ciliates (ciliophora), 73
313, 314 Ciliocytophthoria, 28–29
eosinophilic pleocytosis, 206 CMV. See Cytomegalovirus (CMV)
lymphocytic pleocytosis, Coccidian diseases, 74
206, 209 Coccidioides, 63, 66
Index 383
Coccidioidomycosis potential pitfall, 354

ancillary studies, 146–147 vegetable parenchymal
clinical features, 144 cells, 353
cytomorphologic features, 144–145 Coronavirus, 44
differential diagnosis, 145 Cresyl violet acetate, 326
microbiology, 143–144, 146 Cryptococcal meningitis
Condyloma accuminatum ancillary studies, 219
(anogenital warts), 92 clinical features, 218
Conidia, 55 cytomorphologic features,
Contaminants and mimics 218–219
animal differential diagnosis, 219
carpet beetles, 373, 375 microbiology, 217
dust mites, 373, 375 Cryptococcosis, pulmonary
insects, 373, 374 infections
invertebrates, 373 ancillary studies, 143
artifacts, 351 clinical features, 143
bacterial infection, 356–357 cytomorphologic features, 143
endogenous and exogenous microbiology, 142–143
structures, 352, 353 pneumonia, 144, 145
fungal infection Cryptococcus, 56–58
Alternaria spp., 357, 358 Cryptococcus neoformans
ancillary studies, 363 in CNS infections, 217
calcification, 362, 364 lymph node infections, 242, 243
cytomorphological features, Cryptosporidiosis, in gastrointestinal
358, 361 infections
fungal contaminants, 357, ancillary studies, 171
358, 359 cytomorphologic features, 169
Histoplasma capsulatum, 361 differential diagnosis, 170
myospherulosis, 362 gastric brushing specimen, 170
pollen grains, 362, 363 immunocompetent patients, 169
red blood cell, 358, 360 Cryptosporidium spp., 75
spermatozoa, 360 Crystal formation, 33–34
talc granules, 361, 362 Curschmann spirals, 364, 365
parasitic infection Cutaneous mycoses
(see Parasites, mimics botryomycosis, 271
and contaminants) dematiaceous fungi, 267, 270–271
plant dermatophytosis, 266, 270
algae, 371–373 mycetoma, 271
ancillary studies, 373 sporotrichosis, 270
asterosclereids, 369, 370 Cutaneous parasites
pollen grains, 370 cysticercosis, 272
sporangia, 371 leishmaniasis, 271–272
trichomes, 370, 371 parasitic infections, 271
viral infection Cysticercosis, 272
ancillary studies, 354 Cytology, 5
cellular degeneration, 353 FNA, 2
koilocytes, 352 infections, diagnosis of, 2
384 Index
Cytology (cont.) E
microorganisms, 2 Echinococcosis. See Hydatid disease
molecular studies, 1, 3 Echinococcus granulosus, 79, 80
routine stains spleen infections, 255
H&E stain, 323 Emperipolesis, 26–28
Pap stain, 322 Empyema, pleural infections
Romanowsky stains, 322 and, 159
Toluidine blue, 323 Entamoeba, 156–157
specimen Enterobius vermicularis, 79–81
diagnosis, 2 ancillary tests, 118
procurement, 1 clinical features, 117
triage, 2 cytomorphologic features, 117
Cytomegalovirus (CMV), 42 diagnosis, 117–118
clinical features, 99–100 microbiology, 117
cytomorphologic features, 100 Eosinophilia
diagnosis, 100 and allergic mucin
gastrointestinal infections ancillary studies, 16
ancillary studies, 167 Charcot-Leyden crystals, 16
cytomorphologic features, cytomorphologic features, 15
165–166 differential diagnosis, 15
differential diagnosis, pleocytosis, 207
166–167 Epstein–Barr virus (EBV), 42, 43
endothelial cells, 165, 166 mesenchymal tumors, 316–317
esophageal brushing, related lymphadenopathy (see
165, 166 Infectious mononucleosis
lymphadenitis, 249–250 lymphadenitis)
microbiology, 99 Eye infection
Molluscum contagiosum, bacterial, 296
99, 100 chlamydial, 296
pulmonary infections, 125–127 fungal, 296–297
urinary tract infections, 193 parasitic, 297–298
Pththirus pubis, 294
viral ophthalmic infections, 295
D
Daphnia, 373
Decoy cells, in BK polyomavirus, F
194, 195 Female genital tract infections, 85, 86
Dematiaceous fungi, 69–70 Filamentous bacteria, 51–53
Demodex folliculorum, 265 Filariae, 81–82
Dermatophytes, 70 Fine needle aspiration (FNA), 2, 9–10
Dermatophytosis, 266, 270 of hydatid cyst fluid, 180
Diatoms, 371–372 of Nocardia pneumonia, 134
Dieterle stain, 327 Flagellates (Mastigophora), 71–73
Diffuse infiltrative lymphocytosis Fluids, 9, 12
(DILS), 308 Flukes. See Trematodes (flukes)
Dirofilariasis, 153–154 Fluorescent stains
Donovanosis, 106, 107 Candida, 342
Index 385
Mycobacterium tuberculosis, calcification, 362, 364

342, 343 cytomorphological features,
Pneumocystis jirovecii, 341 358, 361
FNA. See Fine needle aspiration fungal contaminants, 357,
(FNA) 358, 359
Follicular (lymphocytic) Histoplasma capsulatum, 361
cervicitis, 87 myospherulosis, 362
Follicular cystitis, 192 pollen grains, 362, 363
Follicular dendritic cell sarcoma, red blood cell, 358, 360
317, 318 spermatozoa, 360
Fontana-Masson stain, 331 talc granules, 361, 362
Free-living amebae, 71 morphology, 55
Freshwater red algae, 372, 373 osteomyelitis, 273
Freshwater water fleas, 373 Pneumocystis, 68, 69
Fungi, 7, 9 pulmonary infections
Aspergillus, 58–60 aspergillosis, 147–149
Candida, 55–57, 110–112 blastomycosis, 142
casts, 184, 188 candidiasis, 138–140
conidia, 55 coccidioidomycosis, 143–147
Cryptococcus, 56–58 cryptococcosis, 142–143
dematiaceous, 69–70 histoplasmosis, 140–141
dermatophytes, 70 morphology of, 138
dimorphic fungi, 55 mucormycosis
Blastomyces, 61, 63, 66 (zygomycosis), 149–150
Coccidioides, 63, 66 pneumocystis, 150–152
Histoplasma, 66–67 stains
morphology of, 64–65 characteristics, 328, 330
Paracoccidioides, 66 Fontana-Masson stain, 331
Penicillium, 68 urinary tract infections
Sporothrix, 66, 67 acute candida cystitis, 199
esophagitis ancillary studies, 198–199
ancillary studies, 162–163 clinical features, 198
Candida, 163 cytomorphologic features, 198
cytomorphologic features, differential diagnosis, 198
162, 163 microbiology, 197
differential diagnosis, 162 yeasts, 54, 64–65
immunocompetent and zygomycetes, 59–63
immunocompromised
patients, 161
eye infection, 296–297 G
hyalohyphomycosis, 70 Gastrointestinal system infections, 11
hyphae, 54 anal Pap test, 176, 177
kidney infections, 188–189 cryptosporidiosis, 169–171
lymphadenitis, 242–244 cytomegalovirus, 165–167
mimics diagnosis of, 161
Alternaria spp., 357, 358 fungal esophagitis, 161–163
ancillary studies, 363 giardiasis, 171–172
386 Index
Gastrointestinal system (cont.) female genital tract, 85, 86

Helicobacter pylori gastritis, follicular (lymphocytic)
167–169 cervicitis, 87
herpes simplex viruses, 163–165 Leptothrix vaginalis, 90–91
microsporidiosis, 172–174 normal flora, 87–90
Mycobacterium avium complex Pap tests, inflammatory cells, 88
(MAC), 174–176 parasitic infections
Genital tract, 10 Enterobius vermicularis,
Giardia, 71 117–118
Giardiasis, 171–172 schistosomiasis, 115–117
Giemsa/Gimenez stain, 326, 332 Trichomonas vaginalis,
Gram-positive and Gram-negative 112–114
bacteria, 47–49 Phthirus pubis (insects), 119
Gram stain, 324–325 viral infections
Granulomatous inflammation cytomegalovirus
ancillary studies (CMV), 99–100
multinucleated foreign herpes simplex virus
body-type giant cell, 18 (HSV), 95–99
necrotizing granulomatous human papillomavirus
inflammation, 19 (HPV), 91–95
neoplasia, 20
non-necrotizing granulomatous
inflammation, 19 H
cytomorphologic features, 17, 20 Haemophilus influenzae, in CNS
differential diagnosis, 17–18 infections, 209
Granulomatous lymphadenitis Hashimoto’s thyroiditis, 285
morphologic patterns, 238, 239 Head and neck infections
necrotizing, 237, 238 ear infections, 298
non-necrotizing, 237 eye infection
Granulomatous mastitis, chronic, bacterial, 296
261–262 chlamydial, 296
Granulomatous sialadenitis, 283 fungal, 296–297
Granuloma venereum, 106, 107 parasitic, 297–298
Gynecological infections Pththirus pubis, 294
acute inflammation, 87 viral ophthalmic
bacterial infections infections, 295
Actinomyces, 104–106 infected embryologic cysts,
bacterial vaginosis 293–295
(BV), 101–103 oropharyngeal infections
Chlamydia trachomatis, cervicofacial actinomycosis,
108–110 287–289
granuloma venereum, 106, 107 HPV transmission, 285
Neisseria gonorrheae, HSV, 286–287
103–104 oral candidiasis, 289–291
tuberculosis (TB), 106–108 peritonsillar abscess, 285
Candida, 110–112 salivary gland infections
epithelial change, 87 acute sialadenitis, 280–281
Index 387
Candida and Cryptococcus, Herpes simplex virus (HSV)

280 gastrointestinal infections
chronic sialadenitis, 281–282 ancillary studies, 165
granulomatous sialadenitis, 283 cytomorphologic features, 164
paramyxovirus, 280 differential diagnosis, 165
Staphylococcus aureus, 279 esophageal brushings, 164
sinonasal infections gynecological infections
invasive fungal, 291 ancillary tests, 99
mucormycosis, 292 clinical features, 96–97
noninvasive fungal, 291 cytomorphologic features, 97
rhinoscleroma, 292 diagnosis, 98–99
rhinosporidiosis, 293 microbiology, 95–97
thyroid gland infections keratitis, 295
anaplastic carcinoma, 285 lymph node infections, 247
granulomatous thyroiditis, 285 oropharyngeal disease, 305–306
infective thyroiditis, 283, 284 oropharyngeal infections, 286–287
Helicobacter pylori pulmonary infections
bacterial stains, 325–326 ancillary studies, 124–125
gastritis BAL specimen, 124
ancillary studies, 168–169 clinical features, 123
cytomorphologic features, 167 cytomorphologic features, 123
differential diagnosis, 168 differential diagnosis, 124
mucosal biopsy, 167, 168 measles pneumonia, 125
Helminths (parasitic worms), 76–82 types 1 and 2 (HSV–1 and
Hematologic infections HSV–2), 40, 42
cytomorphologic patterns, urinary tract infections, 192
231, 232 Herpesvirues, 40–43
lymph node (see Lymph node High-grade squamous intraepithelial
infections) lesion (HSIL), 93, 94
spleen Highly active antiretroviral therapy
bacilliary peliosis, 252 (HAART), 302
hydatid cyst, 254–255 Histoplasma, 66–67
infectious mononucleosis, Histoplasmosis, in pulmonary
254–255 infections
mycobacterial infection, ancillary studies, 141
253–254 clinical features, 140
splenitis and splenic cytomorphologic features, 140
abscess, 253 differential diagnosis, 140–141
Hematoxylin and eosin (H&E) microbiology, 140
stain, 323 Hodgkin lymphoma, 310
Hemophagocytosis and Host reactions, to infection, 14
emperipolesis acute (purulent) inflammatory
ancillary studies, 28 response, 13–15
cytomorphologic features, 27 ciliocytophthoria, 28–29
differential diagnosis, 27 crystal formation, 33–34
Hepatic amebic abscess, 178 eosinophilia and allergic
Hepatitis viruses, 46 mucin, 15–16
388 Index
Host reactions, to infection (cont.) p16 immunocytochemistry,

granulomatous inflammation, 95, 96
16–20 urinary tract infections, 192, 194
hemophagocytosis and Hyalohyphomycosis, 70
emperipolesis, 26–28 Hybrid capture II assay, 344, 345
impaired cell-mediated Hydatid cyst, 255
immunity, 25 Hydatid disease
inflammatory pseudotumor cytomorphologic features,
reaction, 32–33 179–180
IRIS, 25–26 differential diagnosis, 180
malakoplakia, 30–32 fine needle aspirate of, 180
necrosis, 21–22 pulmonary infections, 157–158
reactive epithelial and Hyphae, 54
mesenchymal repair, 23–24
Splendore-Hoeppli phenomenon,
34–36 I
viral cytopathic effect, 22–23 Immune reconstitution inflammatory
xanthogranulomatous syndrome (IRIS),
inflammation, 29, 30 25–26, 302
HPV. See Human papillomavirus Immunocytochemistry
(HPV) antibodies, 335–337
HSV. See Herpes simplex virus Aspergillus, 335, 338
(HSV) Pap test, 335, 339
Human herpesvirus–8 (HHV8)- p16, for HPV, 95, 96
associated lymphomas Immunosuppressed host
HIV-associated lymphomatous central nervous system disease
effusion, 310, 312 mass lesions, 312
primary effusion lymphoma, meningitis, 310–311
310, 311 progressive multifocal
Human herpesviruses (HHV), leukoencephalopathy,
41, 42 313, 314
Human immunodeficiency virus human immunodeficiency virus
(HIV) infection (HIV) infection, 302
AIDS-defining conditions, human papilloma virus
302, 303 anal disease, 303–304
lymphadenopathy, 250–251, cervicovaginal disease,
304, 305 303–304
Human papillomavirus (HPV) lymphadenopathy, 304–305
anal disease, 303–304 lymphoproliferative disorders
cervicovaginal disease, 303–304 ARL, 309
gynecological infections Hodgkin lymphoma, 310
ancillary tests, 95 human herpesvirus–8
clinical features, 92 (HHV8)-associated
cytomorphologic features, lymphomas, 310
92–94 plasmablastic lymphoma,
diagnosis, 94 309–310
microbiology, 91–92 PTLD, 308–309
Index 389
oropharyngeal disease K
herpes simplex virus, Kaposi sarcoma, spindle cell
305–306 lesions, 316
OHL, 305, 307 Kaposi’s sarcoma-associated herpes
oral candidiasis, 305 virus (KSHV), 42
Penicillium marneffei infection, Kidney infections
299, 300 fungal, 188–189
pulmonary disease pyelonephritis
effusions, 315–316 acute, 183–184
infection, 314 chronic, 184–185
neoplasia, 315 renal tuberculosis, 187–188
renal disease, 316 xanthogranulomatous pyelone-
salivary gland lesions, 306–308 phritis (XPN), 185–187
spindle cell lesions, 316–318 Klebsiella rhinoscleromatis, 292
transplantation, 300–301 Koilocytosis and HPV, 93
Impaired cell-mediated
immunity, 25
Infected branchial cleft cyst, L
293–295 Lactobacilli, 87–89
Infectious mononucleosis Lactol-phenol cotton blue (LPCB)
lymphadenitis, 248–249 stain, 331
Inflammatory pseudotumor reaction Legionella, 137–138
ancillary studies, 33 Leishmania, 72–74
cytomorphologic features, 32 Leishmania lymphadenitis, 245–247
differential diagnosis, 33 Leishmaniasis, 271–272
Influenza viruses, 44 Leprosy
Insects, 119 ancillary studies, 270
In situ hybridization (ISH) bacteriologic index and morpho-
advantages, 335 logic indices, 265, 266
cervix condyloma, 339, 340 clinical features, 267–268
Epstein–Barr virus, 339, 341 cytomorphologic features, 269
infectious mononucleosis., differential diagnosis, 269
339, 340 Mycobacterium leprae, 266
Intestinal amebae, 71 Leptothrix vaginalis, 90–91
Intra-abdominal infections Liver abscesses, 176–179
diagnosis of, 161 Lung infections, 121, 147. See also
hydatid disease, 178–181 Pulmonary infections
liver abscesses, 176–179 Lymph node infections
pancreatitis, 178 acute suppurative lymphadenitis
peritoneal effusion, 181 ancillary studies, 234
IRIS. See Immune reconstitution causative organisms, 231
inflammatory syndrome cytomorphologic features, 233
(IRIS) differential diagnosis, 233–234
cat scratch lymphadenitis,
234–236
J CMV lymphadenitis, 249–250
JC virus (JCV), 45 fungal lymphadenitis, 242–244
390 Index
Lymph node infections (cont.) parasites, 70–82

granulomatous lymphadenitis, viruses, 37–46
237–240 Microfilariae, 81–82
herpes simplex virus Microsporidia, 75
lymphadenitis, 247 Microsporidiosis, 172–174
HIV-associated lymphadenopathy, Mikulicz cells, 292
250–251 Mimics. See Contaminants and
infectious mononucleosis mimics
lymphadenitis, 248–249 Mollaret meningitis
leishmania lymphadenitis, ancillary studies, 216
245–247 clinical and cytomorphologic
lymphogranuloma venereum, 236 features, 215
mycobacterial lymphadenitis, differential diagnosis, 216
240–242 microbiology, 214
toxoplasma lymphadenitis, Molluscum contagiosum, 45,
244–245 99, 100
Lymphocytic pleocytosis, 206, 209 skin infections, 262, 263
Lymphogranuloma venereum, 236 Monocytic pleocytosis, 206
Lymphoproliferative disorders Mucormycosis (zygomycosis)
ARL, 309 ancillary studies, 150
Hodgkin lymphoma, 310 clinical features, 150
human herpesvirus–8 (HHV8)- cytomorphologic features, 150
associated lymphomas, 310 microbiology, 149
plasmablastic lymphoma, sputum specimen, 157
309–310 Multibacillary leprosy, 268
PTLD, 308–309 Multicentric Castleman disease
(MCD), 304
Musculoskeletal system infections,
M 11. See also Bone and
Malakoplakia, 190–191, 193 joint infections
ancillary studies, 32 Mycetoma, 271
cytomorphologic features, 31 Mycobacteria, 48–50, 253–254
differential diagnosis, 32 lymphadenitis
Michaelis–Gutmann bodies, Bacillus Calmette-Guérin
30, 31 (BCG) vaccine, 241
Male genital tract infections, granulomatous inflammation,
202–203 240, 241
Measles, 130–131 tuberculous lymphadenitis, 240
Merkel cell polyomavirus (MCV/ osteomyelitis, 273
MCPyV), 45 spindle pseudotumor, 316
Michaelis–Gutmann bodies, 30, Mycobacterium avium complex
31, 193 (MAC)
Microbiology. See also specific ancillary studies, 175–176
organisms cytomorphologic features,
algae, 82–83 174–175
bacteria, 46–54 differential diagnosis, 175
fungi, 54–70 duodenal brushing specimen, 175
Index 391
Mycobacterium tuberculosis, 49–50 O

CNS infections, 216 Ocular cryptococcosis, 297
hematologic infections, 240 OHL. See Oral hairy leukoplakia
Mycology, 7 (OHL)
Myiasis, 265–266 Oral candidiasis, 289–291, 305
Oral hairy leukoplakia (OHL),
305, 307
N Oropharyngeal infections
Naegleria fowleri, in CNS cervicofacial actinomycosis,
infections, 228 287–289
Neck infections. See Head and neck HPV transmission, 285
infections HSV, 286–287
Necrosis oral candidiasis, 289–291
cytomorphologic features, 21–22 peritonsillar abscess, 285
differential diagnosis and Osteomyelitis, acute, 274
ancillary studies, 22
Necrotizing granulomatous
inflammation, 19 P
Necrotizing granulomatous Pancreatitis, 178
pneumonia, 136 Papanicolaou (Pap) test, 8
Neisseria gonorrheae, in anal, 176, 177
gynecological infections inflammatory cells, 88
ancillary tests, 104 stain, 322
clinical features, 103 Papillomaviruses, 38–39
cytomorphologic features, 103 Paracoccidioides, 66
diagnosis, 103 Paragonimiasis, 154–155
microbiology, 103 Parainfluenza virus, 44, 129–130
Neisseria meningitidis, 209 Parasites
Nematodes (roundworms), 79–82 Apicomplexa, 74–76
Neurocysticercosis, 227 breast infections, 262
Neurosyphilis, 223–225 eye infection, 297–298
Neutrophilic pleocytosis, 206 gynecological infections
Nocardia, 51, 52 Enterobius vermicularis,
pulmonary infections, 133–134 117–118
Nongonococcal uretheritis schistosomiasis, 115–117
(NGU), 203 Trichomonas vaginalis,
Non-necrotizing granulomatous 112–114
inflammation, 19 helminths, 76–82
Nontuberculous mycobacteria mimics and contaminants
(NTM), 50 ancillary studies, 369
Normal flora cellular degeneration,
clinical features, 89 366, 367
cytomorphologic features, ciliocytophthoria, 366–368
89–90 leisegang rings, 368, 369
diagnosis, 90 parasite ova, 366
lactobacilli, 89 worms, 364, 365
microbiology, 87–88 osteomyelitis, 273
392 Index
Parasites (cont.) Pneumonia

protozoa, 70–74 adenovirus, 127
pulmonary infections Cryptococcus, 144, 145
dirofilariasis, 153–154 measles, 125
echinococcosis (hydatid necrotizing granulomatous
disease), 157–158 pneumonia, 136
Entamoeba, 156–157 Nocardia, 134
paragonimiasis, 154–155 tuberculosis, 136
pleural infections and Polymerase chain reaction (PCR)
empyema, 159 amplicons, 345
strongyloidiasis, 154 DNA sequencing and melt curve
Toxoplasma gondii, analysis, 346
155–156 microarray technology, 346, 347
urinary tract infections postamplification analysis and
schistosomiasis, 199–201 reverse hybridization, 346
trichomoniasis, 201, 202 uses, 345
Parasitology, 7 Polyomaviruses, 44–45, 196
Parvoviruses, 46 Posttransplant infections, 300–301
Paucibacillary leprosy, 268 Posttransplant lymphoprolif-
Penicillium marneffei, 68 erative disorder (PTLD),
Peritoneal effusion, with 308–309
infection, 181 Poxviruses, 45
Peritonsillar abscess, 285 Primary amebic meningoencepha-
Phaeohyphomycosis, 271 litis, 228
Phloxine-tartrazine stain, 334 Progressive multifocal leukoen-
Phthirus pubis, 119 cephalopathy, 313, 314
Phycomycosis, 292 Prototheca, 83
p16 immunocytochemistry, for Protozoa
HPV, 95, 96 amebae (sarcodina), 71
Plant contaminants and mimics ciliates (ciliophora), 73
algae, 371–373 flagellates (mastigophora), 71–73
ancillary studies, 373 Pseudo-herpes, Pap test, 354, 355
asterosclereids, 369, 370 Pseudokoilocytes, 352, 354
pollen grains, 370 Pththirus pubis, 294
sporangia, 371 PTLD. See Posttransplant
trichomes, 370, 371 lymphoproliferative
Plasmablastic lymphoma, 309–310 disorder (PTLD)
Pleural infections and Pulmonary infections
empyema, 159 bacterial infections
Pneumocystis, 68, 69 Actinomyces, 132–133
ancillary studies, 152 Legionella, 137–138
clinical features, 151 Nocardia, 133–134
cytomorphologic features, 151 tuberculosis (TB), 135–137
differential diagnosis, 151–152 diagnostic method, 122
microbiology, 150 fungal infections
Pneumocystis carinii, 152 aspergillosis, 147–149
Pneumocystis jirovecii, 323 blastomycosis, 142
Index 393
candidiasis, 138–140 Respiratory viruses, 44

coccidioidomycosis, 143–147 Retroplasia, 353, 355
cryptococcosis, 142–143 Retroviruses, 45–46
histoplasmosis, 140–141 Rhinoscleroma, 292
mucormycosis Rhinosporidiosis, 293
(zygomycosis), 149–150 Rhinosporidium seeberi, 293
pneumocystis, 150–152 Rickettsial stains, 331–332
parasitic infections Romanowsky stains, 322
dirofilariasis, 153–154 Roundworms. See Nematodes
echinococcosis (roundworms)
(hydatid disease), 157–158
Entamoeba, 156–157
paragonimiasis, 154–155 S
pleural infections and Schistosomes, 82
empyema, 159 Schistosomiasis
strongyloidiasis, 154 ancillary tests, 117
Toxoplasma gondii, 155–156 clinical features, 115–116
pneumonia, 121 cytomorphologic features, 116
viral infections dignosis, 116
adenovirus, 126–128 microbiology, 115
cytomegalovirus (CMV), urinary tract infections
125–126 ancillary studies, 201
herpes simplex virus (HSV), clinical features, 200
122–125 cytomorphologic features,
measles, 130–131 200–201
parainfluenza, 129–130 differential diagnosis, 201
respiratory syncytial virus microbiology, 199–200
(RSV), 128–129 Scrofuloderma, 264
Purulent inflammatory response, 14 Seroconversion, 302
cytomorphologic features, 13 Sexually transmitted infection, 85,
differential diagnosis, 15 103, 112. See also Gyne-
Pyelonephritis cological infections
acute, 183–184 Shunt infections, 222–223
chronic, 184–185 Sialadenitis
xanthogranulomatous pyelone- acute
phritis (XPN), 185–187 inflammatory infiltrate, 280
nontyrosine crystalloids,
280, 281
R risk factors, 280
Reactive epithelial and mesenchy- chronic
mal repair, 23–24 acinar cells, 282
Reactive epithelial atypia, 24 differential diagnosis, 281, 282
Reactive lymphocytosis, 214 Signal amplification assay, 344, 345
Renal tuberculosis, 187–188 Sinonasal infections
Respiratory syncytial virus (RSV), invasive fungal, 291
44, 128–129 mucormycosis, 292
Respiratory tract, 10–11 noninvasive fungal, 291
394 Index
Sinonasal infections (cont.) fluids, 9

rhinoscleroma, 292 Pap test (smear), 8
rhinosporidiosis, 293 scrapings, swabs/
Skin infections, 11 impressions, 9
cryptococcosis, 263, 264 Tzanck test, 9
cutaneous mycoses washings, brushings, and
botryomycosis, 271 lavage, 9
dematiaceous fungi, 267, Wet prep, 9
270–271 virology, 6–7
dermatophytosis, 266, 270 Spleen infections
mycetoma, 271 bacilliary peliosis, 252
sporotrichosis, 270 hydatid cyst, 254–255
cutaneous parasites infectious mononucleosis,
cysticercosis, 272 254–255
leishmaniasis, 271–272 mycobacterial infection, 253–254
parasitic infections, 271 splenitis and splenic
Demodex folliculorum, 265 abscess, 253
granulomatous inflammation, 263 Splendore-Hoeppli phenomenon
leprosy (see Leprosy) cytomorphologic features, 35
skin abscesses, 263 differential diagnosis and
slit-skin smear, 262 ancillary studies, 36
spectrum, 262, 268 Splenitis and splenic abscess, 253
tuberculosis, 264 Sporothrix, 66, 67
Tzanck preparation, 262, 263 Sporothrix schenckii, 270
Slit-skin smear, 262 Sporotrichosis, 270
Soft tissue infections. See Skin Squamous intraepithelial lesions
infections (SIL), 92
Specimen collection and handling Streptococcus cocci, 221
bacteriology, 7, 8 Streptococcus pneumoniae, in CNS
cytologic specimens, in microbi- infections, 209
ology laboratory, 8 Strongyloides stercoralis, 80–81, 154
mycology, 7 Suppurative lymphadenitis, acute
parasitology, 7 ancillary studies, 234
sites causative organisms, 231
central nervous system, 11 cytomorphologic features, 233
fluids, 12 differential diagnosis, 233–234
gastrointestinal system, 11
genital tract, 10
musculoskeletal system, 11 T
respiratory tract, 10–11 Taenia, 78–79
skin, 11 Taenia solium, in CNS infections, 227
urinary tract, 10 Tapeworms. See Cestodes
sterile containers/tubes, aspirated (tapeworms)
material, 6 Thyroid gland infections
type anaplastic carcinoma, 285
fine needle aspiration granulomatous thyroiditis, 285
(FNA), 9–10 infective thyroiditis, 283, 284
Index 395
Toluidine blue, 323, 326 bladder

Toxoplasma gondii, 75, 76, bacterial cystitis, 189–192
155–156 malakoplakia, 190–191, 193
CNS infections, 221 fungal, 197–199
lymph node infections, 244, 245 kidney infections
Toxoplasma lymphadenitis, 244–245 acute pyelonephritis, 183–184
Toxoplasmosis, 225–227 chronic pyelonephritis,
Trematodes (flukes), 82 184–185
Treponema pallidum, in CNS fungal, 188–189
infections, 223 renal tuberculosis, 187–188
Trichomonas, 71–72 xanthogranulomatous
Trichomonas vaginalis, 72, 366 pyelonephritis (XPN),
ancillary tests, 114 185–187
clinical features, 113 male genital tract infections,
cytomorphologic features, 202–203
113–114 parasites
diagnosis, 114 schistosomiasis, 199–201
microbiology, 112, 113 trichomoniasis, 201, 202
Trichomoniasis, 113, 201, 202 viruses
Tri-PAS stain, 332 adenovirus, 192
Trypanosoma, 73 BK polyomavirus, 193–197
Tuberculosis (TB) herpes simplex virus
gynecological infections (HSV), 192
ancillary tests, 108 human papillomavirus
clinical features, 106, 107 (HPV), 192
cytomorphologic features, 107 Urine trichomoniasis, 202
diagnosis, 108
microbiology, 106
pulmonary infections V
ancillary studies, 137 Varicella-Zoster virus (VZV), 42
clinical features, 135 Ventriculoperitoneal (VP) shunts, 222
cytomorphologic features, 135 Virology, 6–7
differential diagnosis, 137 Viruses
microbiology, 135, 136 cytopathic changes, 38, 39
pneumonia, 136 cytopathic effect
Tuberculous lymphadenitis, 240, cytomorphologic
305, 306 features, 22–23
Tuberculous meningitis, 216–217 differential diagnosis and
Tzanck test, 9 ancillary studies, 23
cytoplasmic inclusions, 40
gynecological infections
U cytomegalovirus
Urethritis, 203 (CMV), 99–100
Urinary bladder infections herpes simplex virus (HSV),
bacterial cystitis, 189–192 95–99
malakoplakia, 190–191, 193 human papillomavirus
Urinary tract infections, 10 (HPV), 91–95
396 Index
Viruses (cont.) urinary tract infections

hepatitis viruses, 46 adenovirus, 192
herpesvirues, 40–43 BK polyomavirus, 193–197
inclusions, in culture, 7 herpes simplex virus
meningitis (HSV), 192
ancillary studies, 213–214 human papillomavirus
clinical features, 212 (HPV), 192
cytomorphologic features, Volvocales algae, 373
212–213
differential diagnosis, 213
microbiology, 212 W
mimics and contaminants Warthin–Starry stain, 326–327
ancillary studies, 354 Wet mount preparation, 324
cellular degeneration, 353
koilocytes, 352
potential pitfall, 354 X
vegetable parenchymal Xanthogranulomatous inflammation,
cells, 353 29, 30
ophthalmic infections, 295 Xanthogranulomatous
papillomaviruses, 38–39 pyelonephritis (XPN)
parvoviruses, 46 ancillary studies, 187
polyomaviruses, 44–45 cytomorphologic features,
poxviruses, 45 185–186
pulmonary infections differential diagnosis, 186–187
adenovirus, 126–128 histopathology, 185, 186
cytologic features of, 123
cytomegalovirus (CMV),
125–126 Y
herpes simplex virus Yeasts, 54, 64–65
(HSV), 122–125
measles, 130–131
parainfluenza, 129–130 Z
respiratory syncytial virus Ziehl–Neelsen stain, 327, 329
(RSV), 128–129 Zuska disease, 259
respiratory viruses, 44 Zygomycetes, 59–63
retroviruses, 45–46 taxonomy, 60
stains, 332–334 Zygomycosis. See Mucormycosis
tumors (oncogenesis), 38 (zygomycosis)

Cytopathology of Infectious Diseases

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Cytopathology of Infectious Diseases

Dorothy L. Rosenthal, MD, FIAC, Series Editor

For further volumes:

Pam Michelow, MBBCh, MSc (Med Sci)

Walid E. Khalbuss, MD, PhD, FIAC

ISSN 1574-9053 e-ISSN 1574-9061

Library of Congress Control Number: 2011932800

© Springer Science+Business Media, LLC 2011

Printed on acid-free paper

Springer is part of Springer Science+Business Media (www.springer.com)

To my husband Alan and children Gina, Matt, and Aaron.

To my family, mentors, trainees, and friends

Although it is long overdue, finally there is a textbook developed

FNA cytology had a rebirth in the USA due to the contributions of

The subspeciality of cytopathology is over 60 years old and has

and enthusiasm for cytopathology. They bring to the series,

R. Marshall Austin, MD, PhD

Gladwyn Leiman, MBBCh, FIAC, FRCPath

Anil V. Parwani, MD, PhD

We believe that the examination of fluid removed from lymphatic glands

Cytopatholgy provides a rapid, inexpensive, simple, and effective

L. Pantanowitz et al., Cytopathology of Infectious Diseases, 1

●● Specimen triage: Rapid assessment with submission of additional

However, very few books deal with the cytomorphologic features

Cytology is often performed in the investigation of patients with

L. Pantanowitz et al., Cytopathology of Infectious Diseases, 5

Fig. 2.1. Aspirated material obtained by FNA can be submitted by the

●● Virology. Methods used to diagnose viral infections include

Table 2.1. Characteristic viral inclusions observed in culture.

(Table 2.1). Serology (detection of circulating antibodies)

Fig. 2.2. Cytologic specimens received in the microbiology laboratory

●● Wet prep can be performed at the patient bedside to provide

molecular studies. Material submitted for culture requires the

grading system) have been used to assess the quality of sputum

●● Fluids. Effusions due to bacterial infection (e.g., Staphylococcus

The reaction of a human host to infectious stimuli can differ and

Acute (Purulent) Inflammatory Response

L. Pantanowitz et al., Cytopathology of Infectious Diseases, 13

Table 3.1. Different host reactions to infection.

Fig. 3.1. Acute suppurative lymphadenitis (Diff-Quik stain, high mag-

Eosinophilia and Allergic Mucin

Fig. 3.2. Charcot-Leyden crystals (Pap stain, high magnification). Needle-

●● Granulomas may form cohesive clusters of macrophages (e.g.,

●● Granulomas associated with malignancy: Lymphoma, seminoma,

Fig. 3.3. Multinucleated foreign body-type giant cell (Diff-Quik stain,

Fig. 3.5. Necrotizing granulomatous inflammation (Pap stain, medium

Fig. 3.6. Necrosis (Pap stain, low magnification). Necrotic acellular

●● Coagulative necrosis contains ghost cells that have loss of nuclei

Viral Cytopathic Effect

●● Cytoplasmic changes may include giant cell formation and

Reactive Epithelial and Mesenchymal Repair

Fig. 3.7. Reactive epithelial atypia (H&E stain, high magnification). In

groups and maintenance of polarity. High cellularity, loss of

Reactions with Impaired Cell-Mediated Immunity

Immune Reconstitution Inflammatory Syndrome

●● Clinically it presents as a paradoxical worsening of disease or

Hemophagocytosis and Emperipolesis

Fig. 3.8. Hemophagocytosis (Diff-Quik stain, high magnification).

Fig. 3.9. Ciliocytophthoria (Pap stain, high magnification). A detached

Fig. 3.10. Xanthogranulomatous inflammation. FNA showing (left) a

Nontuberculous mycobacteria (NTM), which include all of

Chlamydia trachomatis (previously called TRIC agent). This

s pecies including H. capsulatum. H. capsulatum var. capsulatum