CBME Microbiology Practical Record - Modified - 1

BHIMA BHOI MEDICAL COLLEGE AND HOSPITAL
BALANGIR
DEPARTMENT OF MICROBIOLOGY
PRACTICAL RECORD BOOK
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Certificate
BHIMA BHOIMEDICAL COLLEGE AND HOSPITAL
DEPARTMENT OF MICROBIOLOGY
It is certified that, this is a bonafide record of the practical exercises of
Microbiology done byMiss / Mr _______________________________________
University. Roll. No. ___________________ He/She has attended all the exercises
entered in this record book and his/her progress is satisfactory
Signature of the Teacher in-charge Professor and Head
Name: Department of Microbiology
Date:
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Instructions to Students
1. Be punctual and maintain time specified for each exercise/activity
2. Eating or drinking in the lab at any time is to be strictly avoided
3. Report all accidents, injuries, and breakage of glass or equipment to instructor
immediately.
4. Keep pathways clear by placing extra items (books, bags, etc.) on the shelves or under the
work tables
5. Long hair must be tied back.
6. Do not enter lab without Lab coat. Loose clothing should be secured so that they do not
get caught in a flame or chemicals.
7. Come prepared with prior reading on the assigned experiments before you start to work.
8. Pay close attention to anycautions described in the laboratory exercises
9. Do not taste or smell chemicals.
10. Unauthorized experiments or procedures must not be attempted.
11. Keep solids out of the sink.
12. Do not lean, hang over or sit on the laboratory tables.
13. Handle microscopes with outmost care.
14. Bring muslin clothes for cleaning slides
15. Do not leave your assigned laboratory station without permission of the teacher.
16. Learn the location of the fire extinguisher, eye wash station, first aid kit.
17. Do not lift any solutions, glassware or other types of apparatus above eye level.
18. Learn how to handlethe laboratory materials and equipment safely.
19. Follow all instructions given by your teacher.
20. Leave your work station clean and in good order after your work
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Table of Contents
S.No. Topic Competency Page Score Faculty
(*Certification Skills **AETCOM) No. No. Signature
I General Microbiology, Immunology & Hospital Infection Control
1 A-Introduction to Microbiology laboratory MI 1.1
B - Microscopy MI 1.2
2 1. General principles of Laboratory diagnosis of MI 8.9,
Bacterial diseases.(Sample collection, transportation, MI 8.10
bacterial identification methods in general) MI 8.7
2. Demonstration of respect for patient samples sent MI 8.11
for laboratory investigations**
3. Hand hygiene, PPE- Donning & Doffing of hand MI8.7
gloves (1)*
3 1. Direct methods of bacterial detection MI 1.2
a) Simple staining
b) Hanging drop
2. Gram staining (1)* MI1.2
4 Ziehl-Neelsen staining (1)* MI 1.2
5 Bacterial culture: Culture media, methods and MI 1.1
identification techniques (conventional and automated)
6 Antibiotic sensitivity testing MI 1.6
7 Indirect methods of infectious disease diagnosis MI 1.8, MI
(Immunological diagnostic tests) 8.15
8 General principles of laboratory diagnosis of Viral MI 1.1
diseases
9 1. General principles of laboratory diagnosis of MI 1.2
Parasitic diseases
2. Stool Examination (1)* MI1.2
10 General principles of laboratory diagnosis of Fungal MI 1.1
diseases
11 Hospital infection control – I: Hand hygiene, PPE MI8.5, MI8.6,
(Donning & Doffing) MI8.7, MI8.8
Hand hygiene, PPE (2)* MI8.7
12 Hospital infection control - II: Sterilization & MI8.5, MI8.6,
Disinfection, Biomedical waste management, Needle MI8.7, MI8.8
stick injuries
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II Bloodstream and cardiovascular system infections
13 Laboratory diagnosis of Rheumatic heart disease, MI2.1, MI2.2,
Infective endocarditis and sepsis MI2.3
Gram Stain (2)* MI1.2
14 Laboratory diagnosis of Brucellosis, Leptospirosis, MI4.3, MI8.1
Dengue fever, Scrub typhus, Candidemia
15 Laboratory diagnosis of Enteric fever MI3.3, MI3.4
16 Laboratory diagnosis of Malaria MI2.5, MI2.6
17 Laboratory diagnosis of Filariasis and Leishmaniasis MI2.5, MI2.6
18 1. Laboratory diagnosis of HIV infection MI2.7
2. Confidentiality pertaining to patient's identity in MI8.12,
laboratory result** MI8.14
III Gastrointestinal &Hepatobiliary infections
19 Laboratory diagnosis of Diarrhea MI1.2, MI3.1,
MI3.2
Ziehl-Neelsen staining (2)* MI1.2
Stool Examination (2)* MI1.2
20 Laboratory diagnosis of Dysentery MI1.2, MI3.1,
MI3.2
Stool Examination (3)
21 Laboratory Diagnosis of Intestinal helminthic MI1.2, MI2.4,
infections MI2.5, MI3.1,
MI3.2
Stool Examination (4)* MI1.2
22 Laboratory diagnosis of Hepatic infections MI3.7, MI3.8
IV Skin, soft tissue and musculoskeletal system infections
23 Laboratory diagnosis of skin infections-I MI4.3
(Bacterial: Furuncle, cellulitis, Surgical site infection,
Burn wound infection, Leprosy)
Gram Stain (3)* MI1.2
Ziehl-Neelsen staining (3)* MI1.2
24 Laboratory diagnosis of skin infections-II MI4.3
(Fungal and Viral infections)
25 Laboratory diagnosis of musculoskeletal infections MI4.2
(Arthritis, Osteomyelitis) MI1.2
Ziehl-Neelsen staining (4)*
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V Central nervous system infections
26 Laboratory diagnosis of Meningitis (Pyogenic, MI5.3
Tubercular, Cryptococcal& Aseptic)
* Gram Stain (4) MI1.2
27 Laboratory diagnosis of Encephalitis MI5.3
VI Respiratory tract infections
28 Laboratory diagnosis of Upper respiratory tract MI6.2
infections
Gram Stain(5)* MI1.2, MI6.2
29 Laboratory diagnosis of Lower respiratory tract MI6.2, MI6.3
infections
Ziehl-Neelsen stain (5)* MI1.2, MI6.3
Hand hygiene, PPE (3)* MI8.7
VII Genitourinary & Sexually transmitted infections
30 Laboratory diagnosis of Urinary tract infections MI7.1, MI7.2
31 Laboratory diagnosis of Genitourinary and Sexually MI7.3
transmitted diseases (Urethritis, Genital ulcers)
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BLOCK I
General Microbiology, Immunology &

Hospital Infection Control
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1A.Introduction to Microbiology Laboratory
Competencies
MI1.1: Describe the different causative agents of Infectious diseases and the methods
used in their detection, and discuss the role of microbes in health and disease
MI 1.2: Perform and identify the different causative agents of Infectious diseases by
Gram Stain, ZN stain and stool routine microscopy
Specific Learning Objectives: At the end the session, the students shall be able to,
 Describe the structure and functions of Microbiology laboratory

 Explain the Good laboratory practices
 Demonstrate practice of standard precautions
 Explain the concept of Biosafety in the laboratory
Exercise 1.A:
1. Enumerate various sections/divisions of Microbiology laboratory: describe their
functions and major diagnostic tests carried out in each section.
Section Diagnostic tests done
Bacteriology
Virology
Parasitology
Immunology
Mycology
Molecular biology
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2. Discuss the significance of proper hand hygiene
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3. Enumerate the diseases that can be transmitted through contaminated hands
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4. Suggest the appropriate type of biosafety cabinets to be used in the following scenarios
Scenario Biosafety level
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1B. Microscopy
Specific Learning Objectives: At the end the session, the students shall be able to,
 Enumerate different type of microscopes
 Discuss the applications of various microscopes in diagnostic microbiology
 Focus the compound microscope under various magnification powers
 Handle the microscope with utmost care
Exercise1.B:
1) Enumerate different types of microscopes used in diagnostic microbiology laboratory

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2) Label the parts of microscope in the given picture
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3) Suggest the type of microscope, desired magnification and method used in the following case
scenarios
Case scenario Microscope Magnification Method
Stool examination for

parasitic eggs
Urine examination for pus

cells in a case of Urinary tract
infection
Bacterial examination of CSF

sample in case of pyogenic
meningitis
Bacterial examination of
tissue fluid from gummatous
ulcer in a case of sexually
transmitted disease
4) Write the differences between Electron microscope and the Light/Compound microscope
Features Light/Compound microscope Electron microscope
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Assessment
Sl.No. Student’s performance Score#
1 Comes prepared with requisite prior knowledge 1 2 3

2 Participates actively and contributes to discussion during SGT 1 2 3
3 Shows professional conduct during the Teaching Learning 1 2 3
session
4 Completes the record book activities in time 1 2 3
5 Shows evidence of learning the new skills 1 2 3
(Intellectual/Psychomotor)
Total score /15
(Can be reduced to 5 for convenience)
Faculty Remarks/Feedback:
Date : Faculty Name & Signature
# Mark as 1, 2, 3 for ‘Not satisfactory’, ‘satisfactory’ & ‘Very Good’ respectively
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2. General Principles of Laboratory
Diagnosis of Bacterial diseases
Competencies
MI 8.7: Demonstrate Infection control practices and use of Personal Protective Equipment (PPE)
MI 8.9: Discuss the appropriate method of collection of samples in the performance of laboratory
tests in the detection of microbial agents causing infectious diseases
MI 8.10: Demonstrate the appropriate method of collection of samples in the performance of
laboratory tests in the detection of microbial agents causing Infectious diseases
MI 8.11: Demonstrate respect for patient samples sent to the laboratory for performance of
Specific Learning Objectives:
At the end of the session, the students shall be able to,

 Discuss the need for role of microbiological investigations in diagnosis of infectious
diseases
 Explain the steps in laboratory diagnosis of infectious diseases/syndromes
 Select appropriate clinical specimen in the given case under investigation
 Collect the clinical specimen appropriately
 Identify the essential components of a ‘Sample request form’
 Discuss the significance of prompt transport of a clinical specimen to the laboratory
 Describe the general principles of bacterial culture and identification methods
 Demonstrate respect for patients’ samples received at the laboratory for testing.
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Exercise 2.1:
1) Suggest suitable clinical samples to be collected in the following infections/diseases
Type of infection/disease Suitable Clinical sample to be collected
Conjunctivitis
keratitis
endopthalmitis
Otitis media
Oral and dental infections
Meningitis
Skin and soft tissue infections Aerobic
Anaerobic
Upper respiratory tract infections

(Pharyngitis, tonsillitis, diphtheria)
Lower respiratory tract infections
(Bronchitis, Pneumonia, pulmonary
tuberculosis)
Septicemia
Endocarditis
Diarrhea, Dysentery, Food poisoning
Genital infections (Gonorrhea, syphilis,

chancroid etc.)
Urinary tract infections
Diseases requiring
serological/immunological tests
2) Describe the precautions to be taken while collecting samples for anaerobic culture.
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3) Enumerate the culture media and methods used for anaerobic culture.
Anaerobic culture media Anaerobic culture methods
4) What are the criteria for sample rejection?

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5) What are the general principles to be followed for specimen collection?

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6) Label the blank parts of the packed clinical specimen in the following picture
(Source: Center for Disease Control, Atlanta, USA)
7) Write the general guidelines for specimen transportation
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8) What are the important and essential components of specimen label?
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9) Following is the sample of specimen request form. Please fill the details as per the
clinical case discussion in this practical exercise.
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10) Enumerate the steps used in bacterial culture
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11) Write the methods used for bacterial identification

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12) Write in brief on professional conduct pertaining to the clinical samples

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AETCOM Exercise
Exercise 2.2: Demonstrate respect for patient samples
Competency:
MI 8.11 Demonstrate respect for patient samples sent to the laboratory for performance of

At the end of the module students should be able to
 Describe and apply professional and moral values related to patients’ clinical samples at
the sample reception and processing stage
 Identify the routine events in sample collection, transportation and storage that are
disrespectful to clinical sample.
 Identify the ways to rectify them and demonstrate respect to patients’ samples.
 Describe and demonstrate application of ethical principles and medico legal issues in
laboratory results
In the given situation/case scenario, identify the events that show disrespect / breach in
confidentiality to the clinical sample/ data and suggest ways to rectify them.
1) Biopsy sample of a critical patient getting rejected because it was collected in a formalin
saline
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2) Left over serum sample getting used for research without informed consent
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3) Sample is accompanied with request form with incomplete information/ wrong patient
credentials
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4) Undue delay in testing and reporting of a sample requiring emergency testing

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Assessment

3 Shows professional conduct during the Teaching Learning session 1 2 3
Total score /15
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Certifiable Skill Exercise
Exercise 2.3: Hand hygiene, PPE - Donning & Doffingof hand gloves – (1)
1) Perform hand hygiene appropriately and in the correct sequence
(Source: Essentials of Practical Microbiology, 2nd edition)
2) Write examples of situations requiring hand hygiene in an out patient department

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3) Perform donning and doffing of gloves appropriately
Steps of donning (wearing) gloves.
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Steps of doffing (removal) gloves
4) Write examples of situations requiring use of gloves in an out-patient department

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5) You are about to perform phlebotomy for serological testing. Choose appropriate PPE for the
procedure. Demonstrate the appropriate method of donning and doffing of the selected PPE.
Perform hand hygiene where ever
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Checklist for Assessment of Certification Skill.
Hand hygiene
Step Student’s performance Score YES NO

(Score=0)
1 Removes all hand accessories( finger ringwristwatch. etc.) (0.5) 1.0
and
Applies sufficient amount of soap/hand wash /hand rub (0.5)
2 Rubs palm to palm 0.5
3 Rubs back of palm on Both sides (0.5 + 0.5) 1.0
4 Follows rotational rubbing of thumb on Both sides (0.5 + 0.5) 1.0
5 Rubs back of fingers on palm on Both sides (0.5 + 0.5) 1.0
6 Interlaces fingers in the web spaces 1.0
7 Rubs nails on palms on Both sides (0.5 + 0.5) 1.0
Completes the above steps in 20-40 seconds time or 1.0
Waits till the hands are dried (in case of hand rub)
8 Rinses hands with water 0.5
9 Dries hands with paper with single use towel & (0.5) 1.0
Closes the tap with same paper towel/elbow (0.5)
10 Disposes the paper towel appropriately 1.0
Completes the steps 8, 9 & 10 in 40-60 seconds time 1.0
Total score 10 /10
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Donning (wearing) & Doffing (removal) of Hand Gloves

(Score=0)
Donning Glove:1 Wears by touching and pulling only the edge of 1.0
the cuff
Glove:2 a) Wears by pulling the external surface of 1.0
second glove by
the finger of gloved hand (0.5) and
b) avoids touching the forearm skin (0.5)
Doffing Glove:1 Removes first glove by using the other gloved 1.0
hand, grasps the palm area of the first glove &
peels it off.
Glove:2 a) Holds the removed glove in the other gloved 1.0
hand (0.5) and
b) slides fingers of the ungloved hand under the
other glove at wrist and peels off second glove
over first glove. (0.5)
a) Disposes the gloves appropriately(0.5) and 1.0
b) Performs hand hygiene after gloves removal (0.5)
Total score 5.0 /05
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3. Direct methods of bacterial detection
Competency
MI 1.2: Perform and identify the different causative agents of Infectious diseases by Gram Stain

At the end the session, the students shall be able to,
 Enumerate various types of staining techniques used in bacterial identification
 Describe the principles of simple staining, hanging drop.
 Identify the different causative agents of Infectious diseases by simple staining &
hanging drop.
 Describe the principle of Gram staining
 Perform Gram stain on the smear provided, record the observations with help of a
colored labelled diagram and interpret the findings.
 Identify different causative agents of infectious diseases by Gram Stain
Exercise 3:
1) Record the findings of simple staining
2) Write the clinical applications of simple staining

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3) Record the findings of Hanging drop
4) Write the clinical applications of Hanging drop

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Assessment

Total score /15
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Gram Stain
1) Write the principle of Gram stain
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2) Perform Gram staining, focus under the microscope, record the observations and interpret
the result of Gram staining
Observation
Inference
Examples
Gram positive cocci in clusters Gram positive cocci in chains
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Gram positive cocci in pairs Gram positive bacilli
Gram negative bacilli Gram negative cocci
3) What is the crucial step in the Gram staining and why?

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4) List the differences between Gram positive and Gram negative cell walls
Gram positive cell walls Gram negative cell walls
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5) Write the clinical applications of Gram stain
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Skill certification
Competency No.: MI 1.2 Competency: Gram Stain
Student’s Performance Max. Marks Marks
(05) Scored
Performs skill by following all the steps correctly 02
Focusses the stained slide appropriately 01
Identifies the structures correctly and interprets. 01 (0.5+0.5)
Draws colored labelled diagram of the microscopic field and 01 (0.5+0.5)

writes the report
Score
Rating Rubric Rating
Below expectations (B) (Score – 1, 2, 2.5)
Meets expectations (M) (Score – 3, 3.5)*
Exceeds expectation (E) (Score – 4, 4.5, 5)
CERTIFICATION NO YES
(*Students should secure ‘M’ or ‘E’ to be able to get

Certification in a given skill)
Date Faculty Name & Signature
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4.Ziehl-Neelsen staining
Competency
MI 1.2: Perform and identify the different causative agents of Infectious diseases by ZN stain

 Describe the principles of Ziehl-Neelsen stain.
 Perform Ziehl-Neelsen stain on the smear provided, record the observations by drawing
neat labeled diagram with appropriate colors and interpret the findings.
 Identify different acid fast organisms/structures causing infectious diseases by Ziehl-
Neelsen Stain
 Describe and apply RNTCP grading for suggesting therapy.
Exercise 4:
1) Perform Ziehl-Neelsen staining on the given heat-fixed sputum smear from a 42-year-old
lady with cough with expectoration, evening rise of temperature and loss of weight since 1
month. Focus the smear under microscope, record your observations and interpret the results
Observations
Inference
Examples
2) Describe the principle of Ziehl-Neelsen stain
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3) Enlist various acid fast organisms/structures and the percentage (%) of decolorizer (sulfuric
acid) used for each type.
Acid fast organisms/structures Percentage (%) of decolorizer
4) What is Kinyoun’smethod ? Write its applications.

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5) Write the principle of Ziehl-Neelsen’s stain

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6) Record the observations of Ziehl-Neelsen’s stain
M.tuberculosis M.leprae
Nocardia Coccidian parasites
7) Explain RNTCP grading

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8) Describe the therapeutic implication of RNTCP grading

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Skill Certification
Competency No.: MI 1.2 Competency: Ziehl-Neelsen Stain (1)
(05) Scored

writes the report
Score

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5. Bacterial culture and identification
Competency
MI1.1: Describe the different causative agents of infectious diseases and the methods used in
their detection, and discuss the role of microbes in health and disease
Specific Learning Objectives:At the end of the session, the students shall be able to,
 Explain the purpose of growing the bacteria in the laboratory
 Enlist the basic nutrients required in a culture medium for the growth of bacteria
 Enumerate various culture media used for growing bacteria
 Define different types of culture media (Enriched, Enrichment, Selective, Transport,
differential) and explain their uses
 Suggest the use of suitable culture media based on the type of clinical specimen and
condition
 Enumerate the media, methods and uses of anaerobic culture
 Describe the media, methods and uses of blood culture
 Discuss the principle of automated blood culture systems with examples
 Compare and contrast the conventional from automated blood culture method
 Enumerate the methods/tests used for presumptive identification of bacteria from culture
Exercise 5:
1) Explain the purpose of growing the bacteria in the laboratory

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2) Write the basic chemical constituents in a culture medium

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3) Enumerate different types of transport media and indicate the clinical conditions and type of
bacteria that can be supported by such media
Transport medium Clinical condition Bacteria
Aerobic:
1)
2)
3)
4)
Anaerobic:
1)
2)
4) Define different types of culture media (Enriched, Enrichment, Selective, differential) and
explain their uses
Type of media Examples Uses
Enriched
media:
Enrichment
media:
Selective
media:
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Differential
media:
5) Draw the colored labelled diagrams of culture media (without and with growth) in the space
provided below
Blood agar with Alpha

hemolytic colonies
Blood agar
Blood agar with Beta

hemolytic colonies
MacConkey agar with

Lactose fermenting
Mac Conkey colonies
agar
Mac Conkey agar with

non-lactose fermenting
colonies
Potassium tellurite agar

Chocolate Agar
with black colored
colonies
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Loeffler’s Serum Slope Lowenstein Jensen medium
TCBS agar Deoxycholate citrate

agar
6) What is blood culture? Enlist the media, methods and uses of Blood culture
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7) Enumerate the automated blood culture systems. Add a note their principle
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8) Discuss the advantages and limitations of conventional and automated blood culture systems
Blood culture system Advantages Limitations
Conventional
Automated
9) List the anaerobic culture media
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10) Describe the anaerobic culture methods and write their uses.
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11) Give examples for presumptive identification of bacteria based on colony characteristics.
Colony characters Probable bacteria
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12) Enumerate the biochemical tests used for presumptive identification of bacteria.
13) Draw the colored labelled diagrams of key biochemical tests (Positive and Negative) in the
space provided below and write examples
a) Catalase Test b) Oxidase test
+C T -C
c) Indole test
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Assessment

session
Total score /15
46
6. Antibiotic sensitivity testing
Competency
MI1.6: Describe the mechanisms of drug resistance, and the methods of antimicrobial
susceptibility testing and monitoring of antimicrobial therapy
 Discuss the clinical significance of drug resistance in bacteria.
 Describe the methods of antimicrobial susceptibility testing in the laboratory
 Enumerate the antimicrobials to be used against Gram positive and Gram negative group
of bacteria
 Interpret the antimicrobial susceptibility test results and suggest therapy
Exercise6:
1) Explain the significance of antimicrobial susceptibility testing in the laboratory

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2) Describe the principle and utility of Kirby Bauer Disc diffusion test
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3) Draw a labeled diagram of Kirby Bauer Disc diffusion test with zones of inhibition indicating
sensitive (S), resistant (R) and intermediate (I) results.
Resistant (R) Sensitive (S)
Intermediate (I)
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4) Write the recommended antimicrobials to be used against Gram positive and Gram negative
bacteria
Bacteria Antibiotics
Gram positive
Gram negative
5) List the first, second line and the reserved antibiotics used against gram negative bacilli
Category Antibiotics
First line
Second line
Reserved
6) Explain what do sensitive (S), resistant (R) and intermediate (I) mean in the antimicrobial
susceptibility test reports?
Sensitive (S)
Resistant (R)
Intermediate (I)
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7) Describe the principle and utility of Minimum Inhibitory Concentration technique (MIC) test.
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8) Describe the principle and utility of Epsilometer/E-test.

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9) Draw a labeled diagram of Epsilometer/E-test
10) Enumerate the automated methods available for antimicrobial susceptibility testing
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Assessment

session
Total score /15
50
7. Indirect methods of disease diagnosis
(Immunological tests)
Competencies
MI1.8: Describe the mechanisms of immunity and response of the host immune system to
infections
MI8.15: Choose and interpret the results of the laboratory tests used in diagnosis of the infectious
diseases
 Enumerate different immunological tests available for diagnosis of infectious diseases
 Describe the principle, types and application of Agglutination test
 Describe the principle, and application of Precipitation test
 Describe the principle, application of ELISA test
 Describe the principle, types and application of Immunofluorescence test
 Discuss the principle, Rapid Point of Care (POC) tests with examples.
Exercise 7:
1) List various types of immunological tests available for the diagnosis of infectious diseases
Conventional methods Newer methods
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2) Describe the principle, types and applications of agglutination tests
Agglutination testprinciple:
Types Examples Application
3) Describe the principle, types and applications of precipitation tests
Precipitation test principle:
52
4) Describe the principle, types and applications of ELISA
ELISA principle:
5) Draw colored labeled diagrams of principle of Antigen and Antibody detection ELISA
reactions in the space provided below.
Sandwich ELISA Indirect ELISA
53
6) Describe the principle, types and applications of Immunofluorescence test
Immunofluorescence test principle:
7) Draw colored labeled diagrams of Direct and Indirect Immunofluorescence (IF) reactions
below.
Direct IF test
Indirect IF test
8) Discuss the principle of Rapid/ Point of Care (POC) tests with examples.
Rapid testprinciple:
9) Following are the results of immuno-chromatographic test for Hepatitis B infection done on
three cases. Interpret your results and report (C=Control band, T=Test)
54
Case Result Report
A C T
B C T
C C T
Assessment

session
Total score /15
55
8. General principles of Laboratory
diagnosis of Viral diseases
Competency
MI1.1: Describe the different causative agents of Infectious diseases and the methods used in
 Discuss the purpose of laboratory diagnosis of viral infections
 Describe how the laboratory diagnosis of viral infections differ from bacterial disease
diagnosis
 Discuss the general steps in the diagnosis of viral infections
 Enumerate the direct and indirect methods for diagnosis of viral infections
 Describe Polymerase Chain Reaction and its role in laboratory diagnosis of viral
infections
Exercise 8:
1) Explain the need for laboratory diagnosis of viral infections

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2) Write the differences between laboratory diagnosis of viral infections and bacterial infections
Viral diagnostic methods Bacterial diagnostic methods
56
3) Enumerate the direct and indirect methods for diagnosis of viral infections with examples
and their applications
Viral Examples Applications

diagnostics
Direct
methods
Indirect
methods
4) What is the principle of Polymerase Chain Reaction (PCR)? Discuss its applications.
Principle of
PCR
Applications
57
Assessment

session
Total score /15
58
diagnosis of parasitic diseases
Competency
MI 1.2: Perform and identify the different causative agents of infectious diseases by Gram Stain,
ZN stain and stool routine microscopy
 Describe general steps in the laboratory diagnosis of parasitic infections
 Discuss the types of clinical specimen used in the laboratory diagnosis of parasitic
infections
 Diagnose the underlying parasitic infection based on the history and clinical symptoms
and suggest the suitable laboratory test in the given case.
 Perform saline and iodine mount from the given stool sample and identify various
morphological forms of parasites.
 Identify various parasitic forms in the peripheral smear.
 Describe the role of immunological tests in the diagnosis of parasitic diseases.
Exercise 9:
1) Describe general steps in the laboratory diagnosis of parasitic infections

________________________________________________________________
________________________________________________________________
________________________________________________________________
________________________________________________________________
________________________________________________________________
2) Describe the collection of stool specimen for parasitic examination

________________________________________________________________
________________________________________________________________
________________________________________________________________
________________________________________________________________
________________________________________________________________
________________________________________________________________
________________________________________________________________
59
3) Enumerate different types of clinical specimen (other than stool) used for diagnosis of
parasitic infections and indicate the clinical conditions.
Specimen Clinical condition/s
4) Draw the colored labeled diagrams of common parasitic form seen in stool
60
5) Draw the colored labeled diagrams of common parasitic form seen in peripheral blood smear
6) Enumerate immunological tests used in the diagnosis of parasitic infections and their
applications.
Immunological tests Applications
61
Assessment

session
Total score /15
62
Exercise 9.2: Stool Examination
A lady aged 22 years complains of abdominal discomfort and altered bowel habits since
one week. She has submitted stool sample. Perform stool examination to look for parasitic
elements. Record your observations and interpret the results.
Observations
Inference
63
Skill Certification
Competency No.: MI 1.2 Competency: Stool Examination (1)
(05) Scored
Focusses the preparation appropriately 01

writes the report
Score

64
diagnosis of fungal diseases
Competency
MI1.1: Describe the different causative agents of Infectious diseases and the methods used in
 Recognize the need for laboratory diagnosis of viral infections
 Enumerate major fungal pathogens and the infections/diseases caused by them
 Identify major fungal pathogens based on the morphology (yeast, molds etc.)
 Discuss general steps involved in the diagnosis of fungal infections
 Enumerate the common fungal culture media
 Enlist common tests/methods for fungal identification.
 Compare and contrast the laboratory methods used in the diagnosis of fungal infections
with bacterial infections
Exercise 10:
1) Explain the need for laboratory diagnosis of fungal infections

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2) Enumerate major fungal pathogens and the infections/diseases caused by them
Fungi Infection/Disease caused Fungi Infection/Disease caused
65
3) Draw colored labeled diagrams of major morphological classes of fungi
Yeast Yeast like
Molds Dimorphic
4) Write the common fungal culture media and their uses
Culture media Uses
66
5) Write the common fungal identification tests/methods and their uses
Identification tests/methods Uses
6) Draw a labeled diagram of the microscopic appearance of a dermatophyte in KOH mount.
7) Draw a labeled diagram of the microscopic appearance of a mold in LPCB mount.
67
8) Write the differences between laboratory methods used for the diagnosis of fungal infections
and bacterial infections
Fungal diagnostic methods Bacterial diagnostic methods
Assessment

session
Total score /15
68
11. Hospital infection control I: Hand
hygiene, PPE (Donning & Doffing)
Competencies
 MI8.5: Define Healthcare Associated Infections (HAI) and enumerate the types. Discuss the
factors that contribute to the development of HAI and the methods for prevention
 MI8.6: Describe the basics of Infection control
 MI8.7: Demonstrate Infection control practices and use of Personal Protective Equipment
 MI8.8: Describe the methods used and significance of assessing the microbial contamination
of food, water and air
Specific Learning Objectives; At the end the session, the students shall be able to,
• Describe the need for performing hand hygiene
• Enumerate types of hand hygiene based on the materials used in each type
• Choose appropriate method of hand hygiene in a given situation
• Perform WHO’s my five moments of hand hygiene
• Describe indications and procedure of using PPE
• Choose and perform the personal protective equipment (PPE) in a given simulated
healthcare setting
Exercise 11.1:
1) Perform donning and doffing of various personal protective equipment (PPE) used in in
healthcare setting such as gloves, 3-ply mask, N95 respirator, gown and goggles in the
recommended sequence
Steps of mask donning (wearing).

Source: Essentials of Practical Microbiology, 2nd edition
69
Steps of mask doffing (removal)
Steps of gown donning (wearing).
Steps of gown doffing (removal)

Source: Essentials of Practical Microbiology, 2nd edition
70
Exercise 11.2:
1. Discuss WHO’s my five moments for hand hygiene.
___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
2. What are the products used for hand hygiene?

___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
3. What is relationship between hand hygiene and glove use?

___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
4. What is fit check and discuss its significance?

___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
5. What are the precautions to be followed while removing a mask?

___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
___________________________________________________________
71
6. Name indications where hand wash is necessary and hand rub may not be effective
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
Assessment

session
Total score /15
72
Exercise 11.3: Choose appropriate PPE and demonstrate donning and doffing of the
selected PPE for Blood spill management. Perform hand hygiene wherever appropriate
Checklist for Assessment of Certification Skill
Hand hygiene

(Score=0)
1 Removes all hand accessories ( finger ringwrist 1.0
watch. etc.) (0.5) &Applies sufficient amount of
soap/hand wash /hand rub (0.5)
3 Rubs back of palm on both sides (0.5 + 0.5) 1.0
4 Follows rotational rubbing of thumb on both sides 1.0

(0.5 + 0.5)
5 Rubs back of fingers on palm on both sides (0.5 +0.5) 1.0
7 Rubs nails on palms on both sides (0.5 + 0.5) 1.0

Total score 10 /10

73

(Score=0)
Donning Glove:1 Wears by touching and pulling only the 1.0
edge of the cuff
Glove:2 a) Wears by pulling the external surface 1.0

of second glove by
Doffing Glove:1 Removes first glove by using the other 1.0

gloved hand, grasps the palm area of the
first glove & peels it off.
Glove:2 a) Holds the removed glove in the other 1.0

gloved hand (0.5) and
b) slides fingers of the ungloved hand
under the other glove at wrist and peels
off second glove over first glove. (0.5)

b) Performs hand hygiene after gloves removal
(0.5)
Total score 5.0 /05
74
Sequential Donning (wearing) of PPE
Student’s performance Score YES NO

(Score=0)
Performs proper hand hygiene 1.0
Wears the gown first in sequence 0.25
Wears the gown by fully covering torso from neck to 0.5

knees, arms to end of wrists, and wraps around the back
and fasten it at the waist and back of neck
Wears the mask second in sequence 0.25
Pulls the straps tight and pulls the mask to below chin and 0.5
then applies knots.
Presses on the nasal bridge part of the mask to seal tightly 0.5
and for N95 respirator, performs fit check.
Wears the goggles/face shield third in sequence 0.25
Wears the goggles/face shield by touching the front part 0.5

only
Wears the gloves last in sequence 0.25
Glove:1 Wears by touching and pulling only the edge of 0.5

the cuff

second glove bythe finger of gloved hand (0.25)
Total score 5.0 /05
75
Sequential Doffing (removal) of PPE
(Score=0)
Removes the gloves first 0.5
Does not touch outside of the gloves (contaminated) 0.5
Glove:1 Removes first glove by using the other gloved hand, 0.5
grasps the palm area of the first glove & peels it off.
Glove:2 a) Holds the removed glove in the other gloved hand 0.5
(0.25) and
b) slides fingers of the ungloved hand under the other
glove at wrist and peels off second glove over first glove.
(0.25)
Discards the gloves into red bin 0.5
Performs hand hygiene after gloves removal 0.5
Removes face shield/ goggles second in sequence 0.5
Removes face shield/ goggles by touching the sides only and 0.5
bending forward
Discards face shield/ goggles into red bin 0.5
Does not touch the front part of the gown while removing 0.5
Unfastens the gown ties, taking care that sleeves do not touch the 0.5
body while reaching for ties
Pulls the gown away from neck and shoulders, by touching inside 0.5
of gown only
Turn the gown inside out and rolls it into a bundle and discards 0.5
Discards the gown into yellowbin 0.5
Performs hand hygiene after removal 0.5
Takes off mask fourth in sequence 0.5
Does not touch front part of the mask. 0.5
Unties the lower knot first, then the upper knot and removes the
mask by holding its straps, without touching the front
Discards the mask into yellowbin 0.5
Performs hand hygiene at the last after removal of all PPE 0.5
Total score 10 /10
76
12.Hospital infection control II:
Sterilization & Disinfection, Biomedical
waste management, Needle stick injuries
Competencies
• MI1.4 Classify and describe the different methods of sterilization and disinfection.
Discuss the application of the different methods in the laboratory, in clinical and surgical
practice
• MI1.5 Choose the most appropriate method of sterilization and disinfection to be used in
specific situations in the laboratory, in clinical and surgical practice
• MI8.6: Describe the basics of Infection control
• MI8.7: Demonstrate Infection control practices
• MI8.8: Describe the methods used and significance of assessing the microbial
contamination of food, water and air
Specific Learning Objectives

• Classify the common sterilants and disinfectants used in healthcare settings and describe
their clinical applications
• Discuss the role of central sterile supply department (CSSD)in healthcare settings
• Describe the principles of segregation of biomedical waste
• Demonstrate appropriate segregation of biomedical waste
• Describe the steps of blood spill management
• Describe the principles of respiratory hygiene and cough etiquette
• Describe the methods used and significance of assessing the microbial contamination of
food, water and air
• Interpret the results of common tests performed to assess microbiological contamination
of food, water and air
77
Exercise 12.1:
1) List the clinical applications of steam sterilizer in a healthcare setting

____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
2) List the clinical applications of ethylene oxide sterilizer in a healthcare setting

____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
3) List the clinical applications of plasma sterilizer in a healthcare setting

____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
4) Discuss the unidirectional workflow present in central sterile supply department (CSSD)
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
5) List the clinical applications of membrane filter in a healthcare setting
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
6) List the clinical applications of dry heat sterilizer in a healthcare setting

_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
7. List the clinical applications of glutaraldehyde in a healthcare setting

____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
8. List the clinical applications of alcohol in a healthcare setting

_____________________________________________________________________________
_____________________________________________________________________________
_____________________________________________________________________________
78
9. List the clinical applications of phenol in a healthcare setting
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
10. List the clinical applications of povidoneiodine in a healthcare setting

_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
11. List the clinical applications of Quaternary ammonium compound (QAC)in a healthcare
setting
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
12. Choose appropriate chemical disinfectant/sterilant in various clinical/laboratory situation

S.No. Clinical/Laboratory situation Disinfectant/Sterilant used
13. List the common biomedical waste items generated in healthcare setting that are segregated
in yellow bag.
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
in red bag.
_____________________________________________________________________________
_____________________________________________________________________________
in puncture-proof white/translucent container.
79
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
in puncture-proof blue container.
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
16. Describe briefly the steps of management of blood spill in correct sequence
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
17. Name the components of the respiratory hygiene and cough etiquette?
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
18. Name the methods used for assessing the microbial contamination of water?
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
19. Name the methods used or assessing the microbial contamination of air?
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
20. Enumerate indications for performing environmental surveillance in a healthcare setting?

_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
80
Exercise 12.2: Needle stick injury.
Analyze the case scenarios provided and discuss measures to be taken to prevent transmission of
infection(s) due to needle stick injury in each of them.
A. A 32-year-old staff working in biomedical waste department reported to HICC with

complaints of needle stick injury while segregating a yellow bag. The incident happened 18
hours back. He did not perform any first aid measures at the time of injury. He has not
received any hepatitis B vaccination before. Discuss the post-exposure prophylaxis measures
that should be undertaken.
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
B. A 28-year-old medicine resident reported to HICC with complaints of needle stick injury on
his left thumb while recapping the needle. The incident happened 1 hr back. On enquiry, he
mentioned that he had immediately washed his finger with running tap water for 2 minutes.
The source sample was tested and was found to be positive for hepatitis B surface antigen
and reactive for HIV antibodies. The resident had received a complete course (one series) of
hepatitis B vaccine 10 years back, following which he had an anti-HBs titer of 550 mIU/mL.
Discuss the post-exposure prophylaxis measures that should be undertaken.
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
81
C. A 41-year-old surgeon reported to HICC with complaints of surgical blade injury on his left
thumb, 3 hr back. The source sample was tested positive for hepatitis B surface antigen, but
negative for HIV antibodies and HCV antibodies. The surgeon had received two doses of
hepatitis B vaccine 2 years back. Discuss the post-exposure prophylaxis measures that should
be undertaken
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
_______________________________________________________________________
Assessment

session
Total score /15
82
Block II
Bloodstream and Cardiovascular System
Infections
83
84
13. Laboratory diagnosis of Rheumatic
heart disease, Infective Endocarditis and
Sepsis
Competencies
• MI2.1: Describe the etiologic agents in rheumatic fever and their diagnosis
• MI2.2:Describe the classification etio-pathogenesis, clinical features and discuss the
diagnostic modalities of Infective endocarditis
• MI2.3:Identify the microbial agents causing Rheumatic heart disease & infective
endocarditis

• Enumerate the etiologic agents in rheumatic fever
• Describe the methods of laboratory diagnosis rheumatic fever
• Enumerate the etiologic agents in infective endocarditis
• Describe methods of laboratory diagnosis of infective endocarditis
85
Exercise 13.1:
Clinical case: AnIV drug user developing fever, weakness and cardiac valvularlesions with
new valvular regurgitation in echocardiogram.
1. What is the clinical diagnosis and how you arrived at it?

_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
2. Name the common etiological agents of this clinical condition

_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
3. Describe the diagnostic criteria used for this condition.

_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
4. Describe the procedure to collect specimen for this clinical condition

_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
5. Suggest treatment for this condition

_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
86
Exercise 13.2:
Clinical case: A case of migrating joint pains, subcutaneous nodules and murmur with
ECG finding of prolonged PR interval

_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
2. Name the etiological agent of this clinical condition and the underlying pathogenesis?
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
3. Describe the diagnostic criteria used for this clinical condition.

_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
4. Describe briefly the prevention of recurrence of such episodes

_________________________________________________________________________
_________________________________________________________________________
_________________________________________________________________________
87
Assessment

session
Total score /15
88
Exercise 13.3:
Clinical case: A case with fever, low BP, increased respiratory rate, alerted mentation and
positive blood culture

___________________________________________________________
___________________________________________________________
___________________________________________________________
2. Name scoring system is used to assess the severity of infection and extent of organ failure
___________________________________________________________
___________________________________________________________
___________________________________________________________
3. Name the common etiological agents of this clinical condition

___________________________________________________________
___________________________________________________________
___________________________________________________________
4. Describe the procedure to collect the specimen

___________________________________________________________
___________________________________________________________
___________________________________________________________
5. Describe the laboratory diagnosis of this clinical condition.

___________________________________________________________
___________________________________________________________
___________________________________________________________
6. A heat-fixed smear made from the flagged blood culture bottle is provided. Perform Gram
staining, focus under microscope, record your observations and interpret the results
89
Observations
Inference
Example
Skill Assessment
Competency No.: MI 1.2 Competency: Gram Stain (2)

(05) Scored
Draws colored labeled diagram of the microscopic field and writes 01 (0.5+0.5)
the report
Score

90
14. Laboratory diagnosis of Brucellosis,
Leptospirosis, Dengue fever &Chikungunya,
scrub typhus and Systemic candidiasis
Competencies
• MI8.1: Enumerate the microbial agents and their vectors causing Zoonotic diseases.
Describe the morphology, mode of transmission, pathogenesis and discuss the clinical
course, laboratory diagnosis and prevention
• IM4.3: Discuss and describe the common causes, pathophysiology and manifestations of
Dengue, Chikungunya, and Typhus fever
• Enumerate the microbial agents and their vectors causing Zoonotic diseases
• Describe the clinical manifestations and laboratory diagnosis of brucellosis
• Describe the clinical manifestations and laboratory diagnosis of leptospirosis
• Describe the clinical manifestations and laboratory diagnosis of scrub typhus
• Describe the clinical manifestations and laboratory diagnosis of dengue haemorrhagic
fever
• Describe the laboratory diagnosis of systemic candidiasis
• Interpret the laboratory tests results to diagnose common zoonotic diseases
Exercise 14.1:
Clinical case: A case of remittent fever, with profuse night sweats, arthralgia,
hepatosplenomegaly and positive blood culture
1) What is the clinical diagnosis and how you arrived at it?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2) Explain the mode of transmission of this disease

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
91
3) Interpret the results of the laboratory test displayed
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
4) Suggest other microbiological tests for diagnosis of this condition

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
Exercise 14.2:
Clinical case: A rice-field worker withjaundice, oliguria, respiratory distress and fever
1. Identify the clinical condition and justify your answer

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. Explain the mode of transmission of this disease

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
3. What are the common clinical manifestations observed?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
4.What are the various modalities of laboratory diagnosis?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
92
5. How will you treat this condition?
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
Assessment

session
Total score /15
93
Exercise 14.3:
Clinical case: A patient presented with maculopapular skin rashes, enlarged lymph nodes,
fever and eschar

___________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. What is the etiological agent and how it is transmitted?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
3. What are the clinical manifestations seen in this condition?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
4. What are the various modalities of laboratory diagnosis?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
94
Exercise 14.4:
Clinical case: A case of fever, joint pain, rash and thrombocytopenia

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. List the viruses that cause hemorrhagic fever.

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
95
Exercise 14.5:
Clinical case: An HIV seropositive patient with unexplained weight loss (>10%), fever and
hypotension in whom budding yeast cells were found in blood culture
1. What is the clinical diagnosis and the likely etiological agent?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. Name the risk factors predisposing this clinical condition.

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
3. What are the other clinical manifestations caused by this organism?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
96
Assessment

session
Total score /15
97
15.Laboratory diagnosis of Enteric fever
Competencies
• MI3.3: Describe the enteric fever pathogens and discuss the evolution of the clinical
course, the laboratory diagnosis of the diseases caused by them
• MI3.4: Identify the different modalities for diagnosis of enteric fever. Choose the
appropriate test related to the duration of illness
• Enumerate organisms causing enteric fever
• Describe the clinical manifestations of enteric fever
• Describe the laboratory diagnosis of enteric fever
• Choose appropriate microbiological investigation for diagnosis of enteric fever in
different periods of enteric fever
• Interpret the laboratory tests done for the detection of enteric fever pathogens
• Describe the treatment modalities of enteric fever
Exercise 15.1:
Clinical case: A case of step ladder fever with relative bradycardia and splenomegaly with
positive blood culture

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. How this disease is transmitted?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
98
4. What are the various modalities of laboratory diagnosis in different periods of the disease?
___________________________________________________________
S.No. Period of disease Useful microbiological test
1 1st week
2 2nd week
3 3rd week
4 4th week
5 Carrier

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
6. Interpret the Widal test results (Titers)

S.NO. S.Typhi S.Typhi S.Paratyphi S.Paratyphi Interpretation
O H AH BH
1 20 40 <20 <20
2 160 320 <20 <20
3 320 40 640 <20
4 160 40 <20 <20
5 80 320 160 160
99
Assessment

session
Total score /15
100
16.Laboratory diagnosis of Malaria
Competencies
• MI2.5: Describe the etio-pathogenesis and discuss the clinical evolution and the
laboratory diagnosis of malaria
• MI2.6: Identify the causative agent of malaria

• Enumerate organisms causing malaria
• Describe pathogenesis of malaria
• Describe the clinical manifestations, laboratory diagnosis and treatment of different
types of malaria
• Describe and identify diagnostic forms of malarial parasites in peripheral blood smear
• Interpret laboratory tests to detect malarial parasites
Exercise 16.1:
Clinical case: A case of fever with chills and rigors associated with splenomegaly and
normocytic normochromic anaemia

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. What is the host, infective form, and mode of transmission of the parasite?
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
3. What are the various complications seen?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
4. What is relapse and how it is different than recrudescence?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
101
5. What are the various diagnostic modalities?
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
6. How will you treat this clinical condition?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
7.Drawlabelled diagrams of common diagnostic forms of this parasite focused
102
Assessment

session
Total score /15
103
17. Laboratory diagnosis of Filariasis and
Leishmaniasis
Competencies
• MI2.5: Describe the etio-pathogenesis and discuss the clinical evolution and the
laboratory diagnosis of kala-azar, filariasis and other common parasites prevalent in India
• MI2.6: Identify the causative agent of filariasis

• Describe the clinical manifestations, laboratory diagnosis and treatment of kala-azar
• Describe the clinical manifestations, laboratory diagnosis and treatment of lymphatic
filariasis
• Suggest appropriate sample collection method for laboratory diagnosis of filariasis and
kala-azar
• Identify the diagnostic forms of organisms causing kala-azar and filariasis
Exercise 17.1:
Clinical case: A case with fever, lymphadenopathy, splenomegaly, and hyperpigmentation
on face, hands and feet

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. What is the host, infective form, diagnostic form, and mode of transmission of the parasite?
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
3. What are the other diagnostic tests to diagnose this condition?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
104
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
Exercise 17.2:
Clinical case: A case of fever and unilateral limb swelling

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. What are the etiological agents that can cause this clinical condition?
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
3. Draw a neat, labeled diagram of the etiological agent focused.
105
4. How does man acquire this infection and what is the vector involved?
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
5. Which is the infective stage of the parasite for man?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
6. What are the different modalities of diagnosis of this clinical condition?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
7. Describe the blood collection procedure to demonstrate the organism by microscopy
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
106
Assessment

session
Total score /15
107
18. Laboratory diagnosis of HIV infection
Competencies
• MI2.7: Describe the epidemiology, the etio-pathogenesis, evolution complications,
opportunistic infections, diagnosis, prevention and the principles of management of HIV
• MI8.12: Discuss confidentiality pertaining to patient identity in laboratory results

• Enumerate the modes of transmission of HIV infection
• Describe pathogenesis of HIV infection
• Describe the clinical manifestations, laboratory diagnosis and treatment of HIV
• Interpret the laboratory test results to diagnose HIV infection as per the NACO guidelines
• Enumerate and classify opportunistic infections in HIV/AIDS
• Discuss the importance of maintaining confidentiality pertaining to patient identity in
laboratory results
• Demonstrate maintenance of confidentiality pertaining to laboratory test results in a
simulated setting
Exercise 18.1:
Clinical case: A promiscuous man with chronic diarrhea for more than one month
associated with unexplained weight loss(>10%) and lymphadenopathy

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. What are the various modes of transmission of the etiological agent?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
108
3. What are the different modalities of diagnosis of this clinical condition?
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
4. Which are various opportunistic infections that can occur in this patient?
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
6. Discuss confidentiality pertaining to patient identity in laboratory results.

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
7. What is NACO strategy I and where it is applied?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
8. What is NACO strategy II and where it is applied?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
9. What is NACO strategy III and where it is applied?

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
109
AETCOM Exercise
Exercise 18.2:
Confidentiality pertaining to patient's identity in lab result
Competency
MI 8.14 Demonstrate confidentiality pertaining to patient identity in laboratory results
Specific learning objectives

At the end of the module students should be able to
 Describe confidentiality of patient identity in relation with laboratory investigations
 Identify the routine events in testing and reporting of clinical samples where the
confidentiality of patient identity is applicable.
 Identify the ways to rectify breach in confidentiality in patient identity in relation with
laboratory investigations
 Discuss and apply with justification situations/reasons where breach in confidentiality is
acceptable.
 Describe and demonstrate application of ethical principles and medico legal issues with
respect to confidentiality of patient identity in laboratory results
In a given situation/case scenario, identify the events that show disrespect / breach in
confidentiality to the clinical sample/ data and suggest ways to rectify them.
1) A literate HIV patient getting embarrassed when she finds the test result mentioned on her
case file
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2) Pre-surgical HIV test request received without pre test counseling from surgery ward
110
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
3) You are treating a Covid-19 positive patient and he does not want you to reveal his diagnosis
to others
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
4) A nurse has needle stick injury whileperforming phlebotomy. The patient’s HIV and HBV
status is unknown. The patient is refusing to get tested for HIV
111
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
Assessment

Total score /15
112
BLOCK III
Gastrointestinal and Hepatobiliary
Infections
113
114
19.Laboratory diagnosis of diarrhea
Competencies
 MI 1.2: Perform and identify the different causative agents of Infectious diseases by Gram
Stain, ZN stain and stool routine microscopy
 MI 3.1: Enumerate the microbial agents causing diarrhea and dysentery. Describe the
epidemiology, morphology, pathogenesis, clinical features and diagnostic modalities of these
agents
 MI 3.2: Identify the common etiologic agents of diarrhea and dysentery
Specific Learning Objectives,

At the end of the teaching-learning session the student shall be able to
 Prepare stool wet mount and describe the procedure to screen for parasitic elements
 Perform stool wet mount examination correctly and identify common ova, cyst and larvae
 Define and differentiate diarrhea and dysentery.
 Enumerate common microbial agents causing diarrhea. Classify them based on organism
type, common age group affected and duration of diarrhea
 Enumerate appropriate sample(s) for laboratory diagnosis of infectious diarrhea and describe
the correct method of collection and transportation of such samples to microbiology
laboratory
 Choose appropriate test(s) for microbiological diagnosis of diarrhea
 Analyze a case of diarrhea and suggest a plan of investigation(s) to confirm/rule out common
potential pathogens in that case
 Suggest appropriate sample and microbiological tests along with expected test results to
diagnose a case of suspected cholera
diagnose a case of suspected viral diarrhea
diagnose a case of suspected giardiasis
diagnose a case of suspected opportunistic intestinal parasitic infection
diagnose a case of diarrhea associated with antibiotic administration
 Describe procedure and applications of hanging drop preparation
 Draw and label common parasitic elements seen in stool sample of person suffering from
diarrhea
115
Exercise 19.1:
Clinical case: An outbreak of acute diarrhea with dehydration
1. Identify the probable clinical diagnosis and causative agent.Justify your answer
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
2. Name one simple and quick preliminary diagnostic test for this condition
_____________________________________________________________________
3. Suggest tests to confirm the most probable pathogen
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
4. The patient is in a village and nearest microbiology lab is 20 kms.from there. Describe
appropriate sample collection and transportation procedures for identifying the probable
pathogen. Suggest alternative options for the same
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
5. Based on the clinical features provided and laboratory tests displayed suggest appropriate
treatment in order of preference
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
6. Name 3 other possible pathogens responsible for such condition.

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
116
Exercise 19.2:
Clinical case: A child with diarrhea
1. Identify the most probable pathogen in this case

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. Name other tests to confirm the laboratory diagnosis

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
3. Name the other organisms causing similar clinical manifestations

________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
4. List the laboratory tests to differentiate other pathogens causing this condition
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
5. Describe briefly specific preventive measures for this condition
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
6. A local doctor has prescribed Syp. Amoxycillin-clavulanic acid in appropriate dose and
frequency for 3 days. Is it justified?
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
117
Exercise 19.3:
Clinical case: Diarrhea in a person on antibiotic therapy
1. Identify the probable etiological agent in this case
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
2. Describe the pathogenesis of this condition in brief
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
3. Enumerate other risk factors associated with this clinical condition
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
4. Suggest principles of treating this condition
________________________________________________________________________
________________________________________________________________________
________________________________________________________________________
118
Assessment

session
Total score /15
119
Exercise 19.4:
Clinical case: A case of chronic diarrhea, foul smelling stools with mucus
1. Draw and label the two diagnostic forms of this organism
2. Suggest other samples and tests that can be done to diagnose this clinical condition
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
3. Name the infective form of this organism and mode of transmission
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
4. Enumerate complications of this infection

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
120
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
Exercise 19.5:
Clinical case: An AIDS patient with persistent diarrhea
1. Identify the etiological agent in this case
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
2. Enumerate other similar organisms causing this type of clinical presentation
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
3. List other laboratory tests to diagnose this condition
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
4. Describe the mode of transmission of this infection and suggest preventive measures
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
121
Assessment

session
Total score /15
122
Exercise 19.6:A 46-year-old lady presented with pain abdomen, intermittent diarrhea, lossof
weight, poor appetite and on-and-off fever since 3 weeks. CT scan of the abdomen showed
enlarged mesenteric lymph nodes and minimal ascites. CT guided lymph node aspiration was
done. Heat-fixed smear of the aspirate is provided. Perform suitable staining to demonstrate the
most probable pathogen, focus the smear under microscope, record your observations and
interpret the results
Observations
Inference
Example
123
Skill Certification
(05) Scored

writes the report
Score

124

Clinical Case: A case of diarrhea and abdominal discomfort
1. Give appropriate container and advise the patient on sample collection
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Perform stool examination with the sample provided and record your observations and
Observations
Inference
3. Enumerate more sensitive laboratory tests to diagnose this condition

125
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Describe source and mode of transmission of this infection
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
Skill Assessment

(05) Scored

writes the report
Score

126
20. Laboratory diagnosis of dysentery
Competencies
 MI 1.2: Perform and identify the different causative agents of Infectiousdiseases by Gram
Stain, ZN stain and stool routine microscopy
 MI 3.1: Enumerate the microbial agents causing diarrhea and dysentery.Describe the
epidemiology, morphology, pathogenesis, clinicalfeatures and diagnostic modalities of these
agents

 Define and differentiate diarrhea and dysentery
 Enumerate common microbial agents causing dysentery. Classify them based on organism
type
 Enumerate appropriate sample(s) for laboratory diagnosis of dysentery and describe the
correct method of collection and transportation of such samples to microbiology laboratory
 Choose appropriate tests for microbiological diagnosis of dysentery
 Analyze a case of dysentery and suggest a plan of investigation(s) to confirm/rule out
common potential pathogens in that case
diagnose a case of suspected amoebic dysentery
diagnose a case of suspected bacillary dysentery
 Differentiate amoebic and bacillary dysentery based on macroscopic and microscopic
examination of stool sample
 Draw and label common parasitic elements seen in stool sample of person suffering from
dysentery
127
Exercise 20.1:
Clinical case: A case of frequent blood-stained stools
1. Record your observations of the tests displayed and interpret the results. Identify the
causative agent of this condition
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Enumerate other organisms producing such clinical presentation
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. List laboratory investigations to confirm/refute other organisms listed above
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Enumerate complications of this condition

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
128
Assessment

session
Total score /15
129

Clinical case: A case of frequent dark red offensive-smelling stools
1. Choose appropriate container and advise the patient regarding proper sample collection
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Perform stool examination with the sample provided and record your observation and
inference
Observations
Inference
130
3. Enumerate other investigations to identify/confirm this pathogen
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
4. Enumerate other common pathogens responsible for dysentery

______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
5. Suggest methods to differentiate dysentery caused by two common pathogens
131
Skill Assessment
(05) Scored

writes the report
Score

132
21. Laboratory diagnosis of intestinal
Helminthic infections
Competencies
 MI 1.2: Perform and identify the different causative agents of Infectious diseases by Gram
Stain, ZN stain and stool routine microscopy.
 MI 2.4: List the common microbial agents causing anemia. Describe the morphology, mode
of infection and discuss the pathogenesis, clinical course, diagnosis and prevention and
treatment of the and common microbial agents causing Anemia
 MI2.5: Describe the etio-pathogenesis and discuss the clinical evolution and the laboratory
diagnosis of kala-azar, malaria, filariasis and other common parasites prevalent in India
 MI 3.1: Enumerate the microbial agents causing diarrhea and dysentery
 Describe - the epidemiology, morphology, pathogenesis, clinicalfeatures and diagnostic
modalities of these agents
Specific Learning objectives

 List common microbial agents causing anemia
 Describe morphology of common helminths causing anemia
 Describe laboratory diagnosis of intestinal helminthic infections
 Identify the diagnostic forms (macroscopic and microscopic) of helminths causing anemia
 Enumerate common intestinal helminthic parasites prevalent in India
 Describe morphological forms including diagnostic forms of common intestinal parasites
 Suggest treatment and prevention of intestinal parasitic infections
 Define and differentiate diarrhea and dysentery.
 Enumerate common microbial agents causing diarrhea. Classify them based on organism
type, common age group affected and duration of diarrhea
 Enumerate appropriate sample(s) for laboratory diagnosis of infectious diarrhea and describe
the correct method of collection and transportation of such samples to microbiology
laboratory
 Choose appropriate test(s) for microbiological diagnosis of diarrhea
 Analyze a case of diarrhea and suggest a plan of investigation(s) to confirm/rule out common
potential pathogens in that case
 Perform stool examination to demonstrate diagnostic forms of intestinal parasites
 Draw neat labeled diagrams of diagnostic forms of intestinal parasites
133
Exercise 21.1:
Clinical case: A child who passes a motile fleshy material in stools
1. Identify the material passed in stool by the child. Justify your answer
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
2. Enumerate other laboratory investigations to diagnose/confirm the infection

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
3. Describe briefly – mode of transmission, clinical manifestations and complications

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
4. Draw neat labeled diagram of other diagnostic forms expected in stool microscopy in this
condition
134
Exercise 21.2:
Clinical Case: A malnourished and growth retarded child frequently complaining episodes
of abdominal pain

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
2. Enumerate other laboratory investigations to diagnose/confirm the infection

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
3. Draw a neat labeled diagram of the diagnostic form
4. Describe briefly the mode of transmission, clinical manifestations and complications

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
135
Assessment

session
Total score /15
136
Exercise 21.3:
Clinical case: An incidental stool finding in apparently normal individual
1) Perform stool examination to look for parasitic elements. Record your observations and
Observations
Inference
2) Enumerate other laboratory investigations to diagnose/confirm the infection

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
3) Describe briefly – mode of transmission and complications of this infection

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
4) Suggest appropriate treatment

137
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
Skill Certification
(05) Scored
Focuses the preparation appropriately 01
the report
Score

138
Exercise 21.4:
Clinical case:A child with perianal itching

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
2. Draw neat labeled diagram of the diagnostic form
3. Describe the ideal sample collection method and test done to diagnose this condition
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
4. State the utility of stool examination to diagnose this condition and Justify your answer
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
5. Suggest methods to prevent this infection

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
139
Assessment

session
Total score /15
140
Exercise 21.5:
Clinical case: A female diagnosed withiron deficiency anemia complaining of inflammatory
diarrhea and epigastric pain.
1) Perform stool examination to look for parasitic elements. Record your observations and
Observations
Inference
2) Enumerate more sensitive laboratory investigations to diagnose/confirm the infection

_____________________________________________________________________________
_____________________________________________________________________________
_____________________________________________________________________________
3) Describe briefly – mode of transmission, clinical manifestations and complications

_____________________________________________________________________________
_____________________________________________________________________________
_____________________________________________________________________________
141
4) What can happen if the stool examination is performedafterstoring the sample at room
temperature for 1-2 days?
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
Skill Certification

(05) Scored

writes the report
Score

142
22. Laboratory diagnosis of hepatic
infections
Competencies
 MI3.7: Describe the epidemiology, the etio-pathogenesis and discuss theviral markers in the
evolution of viral hepatitis. Discuss themodalities in the diagnosis and prevention of viral
hepatitis
 MI3.8: Choose the appropriate laboratory test in the diagnosis of viralhepatitis with emphasis
on viral markers

At the end of the teaching-learning session the student shall be able to:
 Enumerate viruses causing hepatitis
 Describe modes of transmission of viruses causing hepatitis
 Describe pathogenesis, clinical features and complications of viruses causing hepatitis
 Describe laboratory diagnosis of viruses causing hepatitis
 Suggest appropriate sample and laboratory diagnostic test for a given case of viral hepatitis
 Interpret the laboratory diagnostic test results of viral hepatitis
 Suggest appropriate measures to prevent viral hepatitis
143
Exercise 22.1:
Clinical case:An outbreak of fever and jaundice
1. List other laboratory investigations to diagnose/confirm this condition and expected results
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Name other organisms that can produce similar presentation

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Suggest tests and expected results to differentiate other organisms causing similar illness
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Explain how other people in the locality could have acquired this infection
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. How is the prognosis of this infection?

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
144
Exercise 22.2:
Clinical case: An intravenous drug abuser with jaundice
1. List modes of transmission of this infection

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Suggest test to know the infectiousness of patient

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Suggest test too know if the infection is acute or chronic

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Suggest measures to prevent this infection

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
145
Exercise 22.3:
Clinical case: A case of fever with jaundice for a few months
1. Comment on the stage and infectivity of the infection

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Enumerate the modes of transmission of this infection

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. How is the general prognosis of this condition?

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Describe briefly the preventive measures of this condition

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Various combinations of serological markers of hepatitis B infection are provided. Interpret

the results and identify the condition
S.No Symptoms HBsAg Anti-HBs Anti-HBc HBeAg Anti-HBe Interpretation
1 Absent + - - - -
2 Present + - IgM + -
3 Present + - IgG - -
4 Absent - + IgG - +/-
5 Absent - + - - -
146
Exercise: 22.4
Clinical Case: An asymptomatic person with an abnormal liver seromarker
1. What is the clinical diagnosis?

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. How this person could have acquired the infection?

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. What are the possible outcomes of this condition?

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Enumerate other tests that can be done to diagnose/confirm this infection

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
Exercise 22.5:
Clinical case: A pregnant lady with jaundice
1. What is the mode of transmission of this infection?

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Describe the prognosis of this condition

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
147
3. Name other viruses causing hepatitis and their modes of transmission
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Describe briefly how infection by other hepatic viruses can be ruled out
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
Assessment

session
Total score /15
148
Exercise 22.6:
Clinical case: A case of tender hepatomegaly associated with fever, weight loss and
jaundice
1. Identify the pathogen

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Describe pathogenesis briefly

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Name other parts of the body where such lesions can be found
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Describe the appropriate sample and its collection procedure to detect the organism
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Name the microbiological tests to confirm this infection

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
149
Exercise 22.7:
Clinical case:A case of cystic hepatic lesion associated with abdominal tenderness and mild
ascitis.
1. Describe the specimen/microscopic features in the smear

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Identify the etiological agent

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Describe mode(s) of transmission and source of this infection

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. List other laboratory tests to diagnose this infection and the expected findings in each of
them
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Name other parts of the body where similar lesions can be seen
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
150
Assessment

session
Total score /15
151
152
BLOCK IV
Skin, Soft Tissue and Musculoskeletal System
Infections
153
154
23. Laboratory diagnosis of bacterial skin
infections
Competency
MI4.3: Describe the etio-pathogenesis of infections of skin and soft tissueand discuss the clinical
course and the laboratory diagnosis

 Enumerate common manifestations of bacterial skin infections
 Enumerate common bacteria causing skin infections
 Classify common bacteria causing skin infections based on the types of lesions
 Enumerate samples and describe the method of collection of samples to diagnose bacterial
skin infections
 Suggest laboratory diagnostic tests to detect common bacterial skin infections and interpret
the results
 Identify the common bacterial pathogens causing skin infections based on the laboratory
test results provided
 Describe pathogenesis and clinical features of common bacterial skin infections
 Suggest treatment and preventive measures for common bacterial skin infections
 Perform acid fast staining to demonstrate Mycobacterium species in skin samples

Exercise 23.1:
Clinical case:A woman with painful breast swelling

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Suggest appropriate sample to diagnose the condition
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
155
3. Record the findings of the tests displayed and identify the organism
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Suggest appropriate antibiotic
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Enumerate the predisposing factors
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
6. Name other common infections caused by this organism
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
7. A heat-fixed smear prepared from the organism isolated from the specimen is provided.
Perform the Gram stain, focus under the microscope, record your observations and interpret the
results
Observation
156
Inference
Examples
Skill Certification
(05) Scored
Focuses the stained slide appropriately 01
the report
Score

157
Exercise 23.2:
Clinical case:A young man with boils on the leg
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Suggest appropriate sample to diagnose the condition
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
_
3. Record the findings of the tests displayed and identify the organism
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Suggest appropriate antibiotic
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Enumerate the predisposing factors for such recurrent lesion
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
158
Exercise 23.3:
Clinical case: A person with discolored limb with bubbles following crush injury
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Suggest appropriate sample to diagnose the condition and briefly describe its collection and
transportation procedure
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Record the findings of the tests displayed and identify the organism(s)
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Suggest other tests to confirm the diagnosis
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Suggest appropriate treatment
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
Exercise 23.4:
159
Clinical case: A diabetic with painful swelling of leg
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
2. Interpret the results and identify the organism
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
3. Suggest appropriate antibiotic for this condition
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
4. Enumerate other common infections caused by this organism
____________________________________________________________________________
____________________________________________________________________________
____________________________________________________________________________
160
Assessment
1`

session
Total score /15
161
Exercise 23.5:
Clinical case: Wound infection
1. Record and interpret the findings of the tests displayed and identify the organism
___________________________________________________________________________
___________________________________________________________________________
_________________________________________________________
2. Name other common organisms causing such infections
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Suggest an appropriate antibiotic
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Briefly describe appropriate sample collection procedure for bacterial culture

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
162
Exercise 23.6:
Clinical case:Burns wound with discharge
1. Record and interpret the findings of the tests displayed and identify the organism
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
2. Name other common organisms causing such infections
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
4. Suggest an appropriate antibiotic
__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________
163
Assessment

session
Total score /15
164
Exercise 23.7:
Clinical case:A case of hypoasthetic skin patch
1. Identify the clinical condition and justify

___________________________________________________________________________
___________________________________________________________________________
2. Describe briefly the sample collection procedure and staining procedure done in this case
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Record your observations, draw a diagram and interpret the results
4. Describe briefly the immunological method to assess the prognosis of this disease
___________________________________________________________________________
___________________________________________________________________________
165
Exercise 23.8:
An 8 year-old child presented with poor appetite, failure to thrive, on-and-off fever since 1
month. On examination cervical lymph nodes were enlarged, matted and nontender. The
overlying skin appeared normal. A heat-fixed smear prepared from the lymphnode aspirate is
provided. Perform the acid fast stain, focus under the microscope, record your observations and
interpret the results.
Observations
Inference
Examples
166
Skill Certification
(05) Scored
the report
Score

167
24. Laboratory diagnosis of fungal and viral
skin infections
Competency
MI4.3: Describe the etio-pathogenesis of infections of skin and soft tissueand discuss the clinical
course and the laboratory diagnosis

 Enumerate common manifestations of viral skin infections

 Enumerate common viruses causing skin infections
 Classify common viruses causing skin infections based on the types of lesions
 Enumerate samples and describe the method of collection of samples to diagnose viral skin
infections
 Suggest laboratory diagnostic tests to detect common viral skin infections and interpret the
results
 Identify the common viral pathogens causing skin infections based on the laboratory test
results provided
 Describe pathogenesis and clinical features of common viral skin infections
 Suggest treatment and preventive measures for common viral skin infections
 Enumerate common manifestations of fungal skin infections
 Enumerate common fungi causing skin infections
 Classify common fungi causing skin infections based on the types of lesions
 Enumerate samples and describe the method of collection of samples to diagnose fungal
skin infections
 Suggest laboratory diagnostic tests to detect common fungal skin infections and interpret
the results
 Identify the common fungal pathogens causing skin infections based on the laboratory test
results provided
 Describe pathogenesis and clinical features of common fungal skin infections
 Suggest treatment and preventive measures for common fungal skin infections
168
Exercise 24.1:
Clinical case:A case of painful perioral lesions with fever
1. Name the clinical diagnosis and the causative agent

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Name the probable sample used for preparing the smear

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Record your observations of microscopy of the lesions and interpret the result
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. What is the mode of spread of this infection and reason for recurrence
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Name other investigations to diagnose this condition

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
169
Exercise 24.2:
Clinical case: A case of generalizedexanthematous skin lesions and fever
1. Identify the most probable clinical condition and the causative agent
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Suggest laboratory investigations to diagnose the infection

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Enumerate viruses causing exanthematous lesions. How are they differentiated from this
infection
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Suggest prevention of this infection

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
170
Exercise 24.3
Clinical case: A case of multiple umbilicatedpapular lesions
1. Identify the clinical condition and the causative agent

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Suggest laboratory investigations to diagnose this condition

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Describe mode(a) of transmission of this infection
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
Assessment

session
Total score /15
171
Exercise 24.4
Clinical case:A case of itchy ring-shaped skin lesions
1. Name the clinical condition

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Study the tests displayed test results, record the observations and identify the organism
3. Describe the procedure of collection and transportation of appropriate sample for the above
test
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Name other organisms causing similar lesions

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Describe mode of transmission

___________________________________________________________________________
___________________________________________________________________________
172
Exercise 24.5:
Clinical case:A case of swollen foot with multiple discharging openings
1. Identify the clinical condition and Justify your answer

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Enumerate organisms causing such lesions

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Describe sample collection procedure

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Suggest treatment
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
173
Exercise 24.6:
Clinical case: A cancer patient with white oral lesions

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Identify the organism and Justify your answer
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Name common species of this organism and describe how the most common pathogenic
species is identified
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Name other lesions caused by this organism

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. Enumerate predisposing factors for this condition

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
174
Assessment

session
Total score /15
175
25. Laboratory diagnosis of
Musculoskeletalinfections
Competency
MI 4.2. Describe the etiopathogenesis, clinical course and discuss thelaboratory diagnosis of
bone & joint infections

At the end of the teaching-learning session the student shall be able to:
 MI 4.2.1. Classify osteomyelitis based on the duration
 MI 4.2.2. Enumerate organisms causing osteomyelitis based on the duration of the infection
 MI 4.2.3. Describe pathogenesis and clinical features of acute and chronic osteomyelitis
 MI 4.2.4. Suggest appropriate samples to be collected and laboratory tests to be performed
for acute and chronic osteomyelitis
 MI 4.2.5. Interpret the laboratory tests performed for diagnosis of acute and chronic
osteomyelitis to identify the etiological agent and choose appropriate treatment
 MI 4.2.6. Enumerate organisms causing arthritis
 MI 4.2.7. Describe pathogenesis and clinical features of septic arthritis
 MI 4.2.8. . Suggest appropriate samples to be collected and laboratory tests to be performed
for septic arthritis
 MI 4.2.9. Interpret the laboratory tests performed for diagnosis of septic arthritis to identify
the etiological agent and choose appropriate treatment
176
Exercise25.1:
Clinical case: A case of painful swollen joint with fever
1. Record the findings and interpret the results

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Enumerate other supportive microbiological tests useful in this condition

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
4. Describe the pathogenesis briefly

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
5. The patient is being administered ceftriaxone. Comment

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
177
Exercise 25.2:
Clinical case: A case of painful swollen joint and skin rashes

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Describe pathogenesis briefly

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
3. Name other tests to confirm the diagnosis and expected results

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
Exercise 25.3:
Clinical case:A case of painful swollen limb with fever after trauma
1. Diagnose the clinical condition

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
2. Identify the causative agent

___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
178
3. List the predisposing factors for development of this condition
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
Assessment

session
Total score /15
179
Exercise 25.4:
Clinical case: An adult with chronic backache and weight loss
1. Diagnose the clinical condition and justify

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
2. Perform Ziehl-Neelsen staining on the given heat-fixed smear. Focus the smear under
microscope, record your observations and interpret the results
Observations
Inference
Example
180
3. Enumerate other tests to diagnose/confirm this condition along with the expected findings
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
4. Suggest investigations to choose most appropriate treatment in this case
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
Skill Certification

(05) Scored
the report
Score

181
182
BLOCK V
Central nervous system infections
183
26.Laboratory diagnosis of Meningitis
Competency
MI 5.3 Identify the microbial agents causing meningitis
At the end of this practical, the students will be able to:

 Enlist pathogens causing infections in Central Nervous System.
 Enlist the appropriate sample to be collected in case of CNS infection
 Describe collection, transport and storage of CSF.
 Identify the microbial agents causing meningitis based upon the macroscopic and
microscopic findings of CSF.
 Choose the appropriate laboratory investigations to be performed for diagnosis of CNS
infections.
 Interpret the results of the laboratory tests performed in diagnosis of the CNS infections.
184
Exercise 26.1:
Clinical Case: A febrile drowsy and irritable child
1. What is the most likely clinical diagnosis in this child? Give reasons
______________________________________________________________________
______________________________________________________________________
2. Suggest investigations to be carried out to confirm the diagnosis
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
3. Keeping the age of patient, enlist probable pathogens in the order of priority.
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
4. Describe the precautions to be taken while collection and transportation of CSF.
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
5. Describe microbiological investigations for diagnosis of meningitis.

______________________________________________________________________
______________________________________________________________________
______________________________________________________________________
185
Exercise 26.2:
Clinical Case: An AIDS patient with fever, headache and stiff neck
1. What is the most probable diagnosis, Justify your answer
___________________________________________________________________
___________________________________________________________________
___________________________________________________________________
2. Draw a labeled diagram of this organism as seen in Indian ink preparation
3. Describe other microbiological investigations that can be done to diagnose this disease.
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
4. Name the media that will be used for isolation of the organism.
186
Exercise 26.3:
Clinical Case: A case of fever, headache and stiff neck
1. Name the possible pathogen
2. Name the media that will be used for isolation of the organism.
3. Enlist the types of infection seen in CNS with their key etiological agents
And mention the differences between CSF findings in various types of CNS infections
Bacterial Viral infection Fungal Parasitic
infections infection infection
Gross examination
Microscopic findings
Biochemical findings
Cell count and
morphology
Any other point
187
4. From another patient with similar complaints CSF culture yielded growth. A heat-fixed
smear prepared from the colonies grown from the specimen is provided. Perform the
Gram stain, focus under the microscope, record your observations and interpret the
results
Observations
Inference
Example
188
Skill Assessment
(05) Scored

writes the report
Score

189
27. Laboratory diagnosis of Encephalitis
Competency
MI5.2: Describe the etiopathogenesis, clinical course and discuss the laboratory diagnosis of
encephalitis

 Enlist pathogens causing encephalitis
 Enlist the appropriate sample to be collected in case of encephalitis
 Choose the appropriate laboratory investigations to be performed for diagnosis of
encephalitis
Exercise27.1:
Clinical case: A case of fever and seizure
1) Suggest investigations that need to be done to confirm the probable

____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
2) How do you differentiate a case of encephalitis from meningitis?
____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
3) Enlist the infective causes of encephalitis and their supportive laboratory findings.
_____________________________________________________________________________________
_____________________________________________________________________________________
____________________________________________________________________________________
190
Assessment

session
Total score /15
191
192
BLOCK VI
Respiratory tract infections
193
194
28. Laboratory diagnosis of Upper
respiratory tract infections (URTI)
Competencies
MI 6.2 Identify the common etiologic agents of upper respiratory tract infections (Gram Stain)
 Enlist pathogens causing infections in respiratory system.

 Describe collection, transport and storage of various respiratory specimens.
 Identify the common etiologic agents of upper respiratory tract infections from Gram stain
smear.
 Choose the appropriate microbiological investigation to be performed in a given case of
URTI.
 Interpret the results of the laboratory tests used in diagnosis of URTI.
 Demonstrations of upper respiratory pathogens like Corynebacterium diphtheria (in Gram
stain, Albert stain), Staphylococcus aureus, Streptococcus pyogenes
195
Exercise 28.1:
Clinical Case: A febrile child with white membrane in throat
1) What is the clinical diagnosis? Justify your answer

______________________________________________________________________________
______________________________________________________________________________
2) Suggest appropriate sample and briefly describe the sample collection procedure to diagnose
this infection
______________________________________________________________________________
______________________________________________________________________________
3) A smear of the sample stained with a special stain is focused. Record your observations and
interpret the results to identify the pathogen in this case.
Observation
Inference
4) Suggest other laboratory tests to confirm the diagnosis
5) Describe prevention of this condition

196
______________________________________________________________________________
______________________________________________________________________________
Exercise 28.2:
Heat-fixed smear of the colonies obtained on blood agar from the sample obtained from the
above case is provided. Perform the Gram stain, focus under the microscope, record your
observations and interpret the results
Observations
Inference
Example
197
Skill Certification
(05) Scored
the report
Score

198
29. Laboratory diagnosis of Lower
respiratory tract infections (LRTI)
Competencies
MI 6.3: Identify the common etiologic agents of lower respiratory tract infections (Including
CoVID-19) (Gram Stain & Acid Fast Stain) Grams Stain-5, Z-N stain-3, hand hygiene, PPE-3
 Enlist pathogens causing infections in Respiratory System.

 Describe collection, transport and storage of various respiratory specimens.
 Identify the common etiologic agents of lower respiratory tract infections from Gram Stain &
Acid fast stained smear.
 Choose the appropriate microbiological investigation to be performed in a given case of
LRTI.
 Interpret the results of the laboratory tests used in diagnosis of LRTI.
 Demonstrations of respiratory pathogens like Streptococcus pneumoniae,
Klebsiellapneumoniae (in Gram stain, colony characteristics, key identification test),
Mycobacterium tuberuculosis (in ZN stain, Growth on LJ media)
Exercise 29.1:
Clinical Case: A case of acute fever and cough with expectoration
(a) Identify the bacterial morphology seen in the Gram stain.
________________________________________________________________________
(b) Name the most likely infective cause of the case, Justify your answer
________________________________________________________________________
199
(c) Describe other microbiological investigations that can be done to confirm the diagnosis of
this case.
______________________________________________________________________
______________________________________________________________________
Assessment

session
Total score /15
200
Exercise 29.2:
Clinical Case: A case of longstanding productive cough with weight loss
1. Write the most likely diagnosis
2. Explain the microbiological investigations that can help you in confirming the
laboratory diagnosis of the disease
3. A heat-fixed smear prepared from the sputum sample of the patient is provided. Perform the
suitable staining procedure, focus under the microscope, record your observations and interpret
the results
Observation
Inference
Example
201
Skill Certification
Competency No.: MI 1.2 Competency: Ziehl-Neelsen stain (5)

(05) Scored
the report
Score

202
Exercise 29.3:
Clinical case: A case of old treated tuberculosis presenting with hemoptysis
1) What is the clinical diagnosis?

___________________________________________________________________________
___________________________________________________________________________
2) Record the observations based on the growth and microscopy demonstrated. Draw a neat-
labeled diagram of the organism and identify.
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
203
3) Differentiate other common species of this organism
4) Enumerate other common infections caused by this organism

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
5) Enumerate predisposing factors for developing such infections
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
204
Exercise 29.4:
You are about to provide care to a patient diagnosed with Covid-19 admitted in an Intensive Care
Unit. Choose appropriate PPE required and demonstrate donning and doffing of the PPE.
Perform hand hygiene wherever appropriate.
Hand hygiene

(Score=0)
1 Removes all hand accessories ( finger ring wrist 1.0
watch. etc.) (0.5) &Applies sufficient amount of
soap/hand wash /hand rub (0.5)
3 Rubs back of palm on both sides (0.5 + 0.5) 1.0
4 Follows rotational rubbing of thumb on both sides 1.0
(0.5 + 0.5)
5 Rubs back of fingers on palm on both sides (0.5 +0.5) 1.0
7 Rubs nails on palms on both sides (0.5 + 0.5) 1.0
Total score 10 /10
205

(Score=0)
Donning Glove:1 Wears by touching and pulling only the 1.0
edge of the cuff
Glove:2 a) Wears by pulling the external surface 1.0

of second glove by
Doffing Glove:1 Removes first glove by using the other 1.0

gloved hand, grasps the palm area of the
first glove & peels it off.
Glove:2 a) Holds the removed glove in the other 1.0

gloved hand (0.5) and
b) slides fingers of the ungloved hand
under the other glove at wrist and peels
off second glove over first glove. (0.5)

b) Performs hand hygiene after gloves removal
(0.5)
Total score 5.0 /05

206
Sequential Donning (wearing) of PPE

(Score=0)
Performs proper hand hygiene 1.0
Wears the gown first in sequence 0.25
Wears the gown by fully covering torso from neck to 0.5

knees, arms to end of wrists, and wraps around the back
and fasten it at the waist and back of neck
Wears the mask second in sequence 0.25
Pulls the straps tight and pulls the mask to below chin and 0.5
then applies knots.
Presses on the nasal bridge part of the mask to seal tightly 0.5
and for N95 respirator, performs fit check.
Wears the goggles/face shield third in sequence 0.25
Wears the goggles/face shield by touching the front part 0.5

only
Wears the gloves last in sequence 0.25
Glove:1 Wears by touching and pulling only the edge of 0.5

the cuff

second glove bythe finger of gloved hand (0.25)
Total score 5.0 /05
207
Sequential Doffing (removal) of PPE
(Score=0)
Removes the gloves first 0.5
Does not touch outside of the gloves (contaminated) 0.5
Glove:1 Removes first glove by using the other gloved hand, 0.5
grasps the palm area of the first glove & peels it off.
Glove:2 a) Holds the removed glove in the other gloved hand 0.5
(0.25) and
b) slides fingers of the ungloved hand under the other
glove at wrist and peels off second glove over first
glove. (0.25)
Discards the gloves into red bin 0.5
Performs hand hygiene after gloves removal 0.5
Removes face shield/ goggles second in sequence 0.5
Removes face shield/ goggles by touching the sides only and 0.5
bending forward
Discards face shield/ goggles into red bin 0.5
Does not touch the front part of the gown while removing 0.5
Unfastens the gown ties, taking care that sleeves do not touch the 0.5
body while reaching for ties
Pulls the gown away from neck and shoulders, by touching inside 0.5
of gown only
Turn the gown inside out and rolls it into a bundle and discards 0.5
Discards the gown intoyellowbin 0.5
Performs hand hygiene after removal 0.5
Takes off mask fourth in sequence 0.5
Does not touch front part of the mask. 0.5
Unties the lower knot first, then the upper knot and removes the
mask by holding its straps, without touching the front
Discards the mask intoyellowbin 0.5
Performs hand hygiene at the last after removal of all PPE 0.5
Total score 10 /10
208
BLOCK VII
Genitourinary & Sexually transmitted
infections
209
210
30. Laboratory diagnosis of Genitourinary
and Sexually transmitted diseases
(Urethritis, Genital ulcers)
Competency
 MI 7.1 Describe the etio-pathogenesis and discuss the laboratory diagnosis of infections of
genitourinary system
 MI 7.2 Describe the etio-pathogenesis and discuss the laboratory diagnosis of sexually
transmitted infections. Recommend preventive measures
Specific Learning objectives :
 Enlist various sexually transmitted pathogens.

 Describe collection, transport and storage of various specimens for diagnosis of
genitourinary &sexually transmitted infections.
 Choose the appropriate microbiological investigation to be conducted in a case of genital
tract / sexually transmitted infection.
 Interpret the results of the microbiological investigation conducted in a case of genital tract /
sexually transmitted infection.
 Counsel a patient of genital tract/ sexually transmitted infection about preventive aspects of
such infections.
211
Exercise 30.1:
Clinical Case: A case of painless genital ulcer
1) What is the most likely clinical diagnosis of the case?
2) Describe the sample collection and laboratory techniques that can be used in the diagnosis of
the disease.
3) Draw the microscopic examination findings from the sample collected from ulcer.
212
Exercise 30.2:
Clinical Case: A case of painful genital lesions
1. What is the most probable clinical diagnosis of the case?
2. Describe the sample collections required for diagnosis of this disease.
3. Describe the microscopic examination that can be performed and draw the diagram.
4. Briefly describe other diagnostic tests for this infection
______________________________________________________________________________
______________________________________________________________________________
213
5. Explain the reason for recurrence of this infection
______________________________________________________________________________
______________________________________________________________________________
6. Enumerate complications of this condition
______________________________________________________________________________
______________________________________________________________________________
Exercise 30.3:
Clinical Case: A woman with vaginal itching and discharge
1. Name the most likely organism seen in the wet preparations.
2. Describe the laboratory diagnosis of this disease.
3. Name other organisms transmitted in the similar manner

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
214
Assessment

session
Total score /15
215
31. Laboratory diagnosis of Urinary tract
infections (UTI)
Competency
MI 7.3: Describe the etio-pathogenesis, clinical features, the appropriate method for specimen
collection, and discuss the laboratory diagnosis of Urinary tract infections

 Enlist pathogens causing infections in Urinary system.
 Describe collection, transport and storage of urine for diagnosis of urinary tract infections.
 Give instructions to patients for mid stream sample collection and transportation.
 Choose the appropriate sample to be collected in a case of UTI (upper/lower UTI)
 Interpret the results of the laboratory tests used in diagnosis of the UTI.
Exercise 31.1:
Clinical Case: A case of fever and burning micturition
1. Identify the culture media, culture technique and purpose of the performing this in diagnosis of
urinary tract infections.
2. Which organisms are probably responsible for the woman’s infection?
216
3. What is the significance of bacterial count in the report of urine?
4. Write instructions that must have been given to her for appropriate sample collection and
transportation.
Exercise 31.2:A young newly married female presented to medicine OPD with increased
frequency and painful urination. She does not have any other complains like fever. Name the
possible pathogens in her case.
Exercise 31.3:A pregnant female was screened during her routine antenatal checkup. Her urine
culture grew Escherichia coli with significant count. Elaborate on the way this report needs to be
interpreted and impact of this on the outcome of pregnancy.
Exercise 31.4:Urine culture of a catheterized adult male with stroke reported growth of two
organisms with significant count but patient is not having any symptoms. Write about your
follow up plan for this case.
217
Assessment

session
Total score /15
218
219

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BHIMA BHOI MEDICAL COLLEGE AND HOSPITAL

PRACTICAL RECORD BOOK

It is certified that, this is a bonafide record of the practical exercises of

Microbiology done byMiss / Mr _______________________________________

entered in this record book and his/her progress is satisfactory

Signature of the Teacher in-charge Professor and Head

Name: Department of Microbiology

General Microbiology, Immunology &

 Describe the structure and functions of Microbiology laboratory

Section Diagnostic tests done

3. Enumerate the diseases that can be transmitted through contaminated hands

Scenario Biosafety level

1) Enumerate different types of microscopes used in diagnostic microbiology laboratory

2) Label the parts of microscope in the given picture

Case scenario Microscope Magnification Method

Stool examination for

Urine examination for pus

Bacterial examination of CSF

Features Light/Compound microscope Electron microscope

Sl.No. Student’s performance Score#

1 Comes prepared with requisite prior knowledge 1 2 3

Date : Faculty Name & Signature

# Mark as 1, 2, 3 for ‘Not satisfactory’, ‘satisfactory’ & ‘Very Good’ respectively

Specific Learning Objectives:

At the end of the session, the students shall be able to,

Type of infection/disease Suitable Clinical sample to be collected

Oral and dental infections

Skin and soft tissue infections Aerobic

Upper respiratory tract infections

Genital infections (Gonorrhea, syphilis,

Anaerobic culture media Anaerobic culture methods

4) What are the criteria for sample rejection?

5) What are the general principles to be followed for specimen collection?

(Source: Center for Disease Control, Atlanta, USA)

7) Write the general guidelines for specimen transportation

8) What are the important and essential components of specimen label?

11) Write the methods used for bacterial identification

12) Write in brief on professional conduct pertaining to the clinical samples

Exercise 2.2: Demonstrate respect for patient samples

Specific Learning Objectives:

4) Undue delay in testing and reporting of a sample requiring emergency testing

1 Comes prepared with requisite prior knowledge 1 2 3

Date : Faculty Name & Signature

# Mark as 1, 2, 3 for ‘Not satisfactory’, ‘satisfactory’ & ‘Very Good’ respectively

(Source: Essentials of Practical Microbiology, 2nd edition)

2) Write examples of situations requiring hand hygiene in an out patient department

Steps of donning (wearing) gloves.

4) Write examples of situations requiring use of gloves in an out-patient department

Step Student’s performance Score YES NO

Date : Faculty Name & Signature

Donning (wearing) & Doffing (removal) of Hand Gloves

Step Student’s performance Score YES NO

Date : Faculty Name & Signature

Specific Learning Objectives:

1) Record the findings of simple staining

2) Write the clinical applications of simple staining

4) Write the clinical applications of Hanging drop

1 Comes prepared with requisite prior knowledge 1 2 3

Date : Faculty Name & Signature