Specimen Collections in The Medical Microbiology and parasitologyNOTES

Specimen Collections in the medical
microbiology and parasitology
BY
LANGLEY ORUTUGU
DEPT. OF MED MICRO AND PARA
QUESTIONS
WHAT IS A SPECIMEN ?
WHAT IS THE DIFFERECNCE BETWEEN A

SPECIMEN AND A SAMPLE?
WHAT IS THE PURPOSE OF SPECIMEN

COLLECTION? WHY?, WHERE?, & HOW?.
WHAT ARE THE SAFETY AND PROPER

PROCEDURES USED IN SPECIMEN
COLLECTION?
WHY?
All diagnostic information from micro & Para
lab is contingent on the quality of specimen
received. A holistic assessment therefore can;
Build a clinical picture of the patient
Confirm disease diagnosis
Inform a treatment plan

Aftermaths of a poorly collected &/or poorly
transported specimen include ;
Failure to isolate the causative agent
Recovery of contaminants or normal flora,

leading to;
 improper patient treatment

Specimen collection Safety considerations
 Follow universal precaution guidelines.
 Treat all specimens as potentially biohazardous.
 Use appropriate barrier protection when

collecting or handling specimens.
 If splashing may occur; protective eyewear, face

masks, and aprons may be necessary.
Don't contaminate external surface of
collection container and/or its accompanying
paperwork.
Minimize direct handling of specimens in

transit.
Use plastic sealable bags with a separate

pouch for the laboratory requisition orders or
transport carriers (for example, small buckets
with rigid handles).
General guidelines for proper specimen
collection
Collect specimen before administering anti-

microbial agents when possible.
Collect specimen with as little contamination as

Possible.
Ensure a representative sample of the infected site.
Utilize appropriate collection devices.

Use sterile equipment and aseptic technique during
invasive procedures.
Clearly label the specimen container.
Collect an adequate amount of specimen.
Develop an understanding of the source

identification schemes.
1. Know when to include “rule-out” request. E.g, the
laboratory may routinely screen for Shigella, and
Campylobacter species in stool cultures but not for
Yersinia or Vibrio species.
If a specimen is to be collected through intact skin,
cleanse the skin first.
Before collection of the specimen, consider the

risk/benefit ration of the collection procedure to the
patient.
Collect specimens in sturdy, sterile, screw-cap, leak

proof containers with lids that do not create an aerosol
when opened.
Consider geographic location and season when
notifying the laboratory of rule out requests. E.g
Coccidioides immitis is endemic in the southwestern

United States, and rotaviruses are more commonly
found in infants and children
in winter.
Identify the specimen source and/or specific site

correctly so that proper culture media will be selected
during processing the laboratory.
General guidelines for proper specimen
transport
______________________________
verification form should include the following
information:
Patient name, age and sex
Patient room number
Physician name
Specific anatomic culture site

General guidelines cont
Date and time of specimen collection
Initials of person obtaining specimen
Antimicrobials, if any, patient is receiving.
When appropriate, include clinical diagnosis,

special culture request,
relevant patient history
Test or procedure requested
General guidelines cont
A separate order is needed for each test,

including anaerobic cultures.
E.g., if sputum is collected for
1.AFB,
2.Fungus and
3.routine culture,
a total of three orders must be entered.

LABELING
1. Each sample must have a label firmly attached to
the specimen container bearing the following
information:
• Date & Time of Collection
• Patient name
• Hospital number or DOB
• Culture site
• Initials of Collector
Patient preparation for Specimen collection
 Review to see if patient has special need

 Identify self to patient politely and professionally
 Patient identity:
1. Inpatient
2. Outpatient
Inspect requisition/ review demographs

Identify collection site and proceedure
TYPE OF MICROBIOLOGY AND
PARASITOLOGY SPECIMENS.
1. Blood
2. sputum
3. Faeces
4. Urine
5. Aspirates
6. Exudates
7. Fluids, e.g; csf, peritoneal, synovial,
marrow
8. Etc.
Blood
Indications for blood collection:
1.Culture.
Type of blood culture
Routine blood culture
Fungus blood culture
Acid fast blood culture –
2.Microscopy
Wet preparation
Staining
Volume:
Blood collection/ sampling methods:
1. Venipuncture
2. Finger prick (capillary)
3. Arterial
Locate a suitable vein before cleansing the

skin.
Sputum
All sputum samples are contaminated to varying degrees with
oropharyngeal secretions. ..
Mechanical rinsing of the mouth immediately before expectoration
will reduce the number of contaminating bacteria.
The patient should rinse his mouth with water, preferably in the
morning.
If unable to get specimen by expectoration, contact respiratory
therapy.
Methods used to facilitate an adequate specimen from patients with
non-productive coughs include:
ultrasonic nebulization with 10% saline Hydration
chest physiotherapy and
 postural drainage.
Cap the container and deliver to the laboratory immediately, as there is

no effective transport medium.
Processing
Order culture.
If ASAP results are desired- a call to the lab is
helpful.
Upon receipt in the laboratory;
Gram-stain microscopically for the presence of
inflammatory and epithelial cells.
Specimens with > 10 squamous epithelial cells
are rejected for culture.
notified nursing unit by telephone when the
sample is unacceptable.
SPINAL FLUID SPECIMENS
Surgical prep and collection by physician required.
Collection method
Lumbar puncture must be performed under conditions
of strict asepsis.
Specimens are transported in sterile screw-cap tubes:
hand carry to laboratory as Emergency specimen.
At least one tube (second or third collection) must be
sent to bacteriology first, before other studies are done.
Obtain “as much as possible”: 4 – 5 ml is optimal for
adults, 0.5 – 1.0 ml in children (additional fluid may be
required if other tests are ordered).
PROCESSING OF SPECIMEN
Order routine culture and specify CSF as the

source.
Do a Gram stain STAT on all spinal fluids.
4. If cryptococcal antigen or viral studies are

desired, order the appropriate tests.
OVA AND PARASITE EXAM
Procedures for recovery of intestinal parasites should
always be performed before barium is used for radiological
examination.
Medications that interfere with the detection of intestinal
protozoa;
a) mineral oil.
b) Bismuth.
c) Antibiotics.
d) antimalarials, and.
e) Non absorbable anti diarrheal preparations.
After administration of any of these compounds, parasitic

organisms may not be recovered for a week to several
weeks.
collected in a clean container & not necessarily
sterile.
specimen should not be contaminated with water or

urine because water may contain free-living organisms
that can be mistaken for human parasites and urine
may destroy motile organisms.
Examination of liquid specimens should occur

within 30 minutes of passage.
It is inappropriate for multiple specimens to be

collected on the same patient on the same day.
MYCOLOGY SAMPLES
1. Skin - Clean site with 70% ethanol.
 Using scalpel, skin scrapings should be made from the active
periphery of the lesion.
 Submit scrapings in a sterile Petri dish or container.
2. Nails - Clean site with 70% ethanol.

Collect shavings and material under the nail plate.
Scrapings should be deep enough to assure acquiring recently
invaded tissue.
Submit nail clippings and scrapings in a sterile Petri dish or
container.
3. Hair –
Use forceps to pluck involved hairs from the edges of the patches.
Submit hair, including shaft, in a sterile Petri dish or container.
Other - Collect and submit specimens as
described for specific type.
Blood - This requires prior laboratory

notification since additional media must
beinoculated at bedside. Order blood fungus
culture.
Urine for culture
General considerations:
Never collect urine from a bedpan or urinal.
Thoroughly clean the urethral opening (and

vaginal vestibule in females) prior to collection.
Use sterile tubes or cups to collect and

transport the urine.
Use soap rather than disinfectants for cleaning

the urethral area.
N/B. If disinfectants are introduced into the urine
during collection
they can inhibit the growth of microorganisms.
Transport the specimen to the laboratory such that it

will be plated within two (2) hours of collection.
If Neisseria gonorrhoeae is suspected;
inoculate a Thayer Martin plate at the bedside.
and transport to the Laboratory immediately.


Preservation
Urines from clinics outside should be place in
tubes with preservative. These specimens can be
held for eight (8) hours.
Alternatively, urines can be refrigerated for 24

hours before plating.
Clean catch urine specimen collection (female):
Cleanse the urethral opening and vaginal

vestibule area using soapy water or clean gauze
pads soaked with liquid soap.
Rinse the area well with water or wet gauze pads.
Hold labia apart during voiding.
Allow a few milliliters to pass.
Collect the midstream portion of urine in a sterile

container.
Clean catch specimen collection (male):
Cleanse the penis
 retract the foreskin (if not circumcised) and

wash with soapy water.
Rinse the area well with water.
Keeping foreskin retracted; allow a few milliliters

of urine to pass.
Collect the midstream portion of urine in a sterile

container.
Ileal conduit urine collection:
 Remove the external urinary appliance and
discard the urine within the appliance.
 Gently swab and clean the stoma opening with

a 70% alcohol pad and then with an iodine solution.
Remove excess iodine with an alcohol pad.
Using sterile technique, insert a double catheter

into the stoma.
Catheterize the ileal conduit to a depth beyond

the fascial level.
Collect the urine drained into a sterile container
.
Indwelling catheter urine collection:
Clean the catheter collection port with a 70%

alcohol swab.
 Using sterile technique, puncture the collection

port with a needle attached to a syringe.
Aspirate the urine and place it into a sterile

container.
.
Straight catheter urine collection:

 Clean the patient's urethral opening
(and in females the vaginal vestibule) with soap,
and carefully rinse the area with water.
Using sterile technique, pass a catheter into the

bladder.
Collect the initial 15 to 30 ml of urine and

discard it.
Collect a sample from the mid- or later flow

of urine in a sterile container.
Urine Pathogens and Specimens Type:
Organism Volume (ml) Specimen Type
Bacteria 0.5-1 After proper cleansing of patient,
collect midstream void.
Fungi 0.5-1 1st morning void is recommended.

Do not collect 24 hour specimen.
Mycobacteria >20 1st morning three consecutive

voided urine specimens are
recommended. Do not collect 24
hour specimen.
Anaerobes 1 Use supra-pubic aspirate.
Virus 10-50 1st morning void is recommended.

Transport to the Laboratory
immediately. Useful for
adenovirus, mumps, and CMV.
Faecal specimens:
Indications for test
Culture
Microscopy
Others
RECTAL SWABS:
indicated for infants or patients acutely ill
Collection Method
Pass the tip of a sterile swab approximately 1
inch beyond the anal sphincter.
Carefully rotate the swab to sample the anal crypts

and withdraw the swab.
Place the swab in transport medium.

ACCEPTANCE AND REJECTION CRITERIA
All clinical specimens must be collected in clean

sterile containers, which must be properly sealed.
The outer portion of the container must not be

Contaminate.
Optimal specimens are aseptically obtained
Specimens consisting primarily of saliva are

rejected.
Swabs should not be used if fluid can be obtained.
Swabs without transport medium are not satisfactory

since they allow drying of the specimen and loss of
viability.
All specimens should be transported to the

laboratory in a sealed zip lock bag.
Rejection criteria of specimens.
Problem / Reasons
1.Unlabeled or improperly labeled specimen:
minor outpatient correction

Date
 time of collection
source and site
These Can be corrected with a call to the doctor’s

office.
 For inpatients;
 a nurse must come to the laboratory and identify
the specimen before it is processed.
 Specimens that are easy to obtain should be

recollected.
 Invasive specimens (e.g. CSF) should be processed

but do not publish results until doctor has been
consulted.
 If the problem cannot be resolved with the nursing

staff, the doctor should be called.
Prolonged transport/Storage
•Urine –
1 hr at room temp, refrigerate, preservative
•Stools for trophozoites – 1 hr collection for soft

formed.
½ hr collection for fluid specimens
•Gonorrhea specimens –
½ hr without transport Medium
Improper container
non-sterile
Leaking container
•Obvious foreign contamination
•Duplicate specimens submitted same time
•Quantity not sufficient (QNS) Blood:

Process, note problem on report.
•Collection/Verification sheet not completely filled out

or patient information doesn’t match sample .

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Specimen Collections in the medical

microbiology and parasitology

WHAT IS THE DIFFERECNCE BETWEEN A

WHAT IS THE PURPOSE OF SPECIMEN

WHAT ARE THE SAFETY AND PROPER

Build a clinical picture of the patient

Confirm disease diagnosis

Inform a treatment plan

Failure to isolate the causative agent

Recovery of contaminants or normal flora,

 improper patient treatment

 Follow universal precaution guidelines.

 Treat all specimens as potentially biohazardous.

 Use appropriate barrier protection when

 If splashing may occur; protective eyewear, face

Minimize direct handling of specimens in

Use plastic sealable bags with a separate

Collect specimen before administering anti-

Collect specimen with as little contamination as

Ensure a representative sample of the infected site.

Utilize appropriate collection devices.

Clearly label the specimen container.

Collect an adequate amount of specimen.

Develop an understanding of the source

Before collection of the specimen, consider the

Collect specimens in sturdy, sterile, screw-cap, leak

Coccidioides immitis is endemic in the southwestern

Identify the specimen source and/or specific site

Patient room number

Specific anatomic culture site

Date and time of specimen collection

Initials of person obtaining specimen

Antimicrobials, if any, patient is receiving.

When appropriate, include clinical diagnosis,

A separate order is needed for each test,

a total of three orders must be entered.

• Date & Time of Collection

• Hospital number or DOB

 Review to see if patient has special need

Inspect requisition/ review demographs

2. Finger prick (capillary)

Locate a suitable vein before cleansing the

Cap the container and deliver to the laboratory immediately, as there is

Order routine culture and specify CSF as the

Do a Gram stain STAT on all spinal fluids.

4. If cryptococcal antigen or viral studies are

After administration of any of these compounds, parasitic

specimen should not be contaminated with water or

Examination of liquid specimens should occur

It is inappropriate for multiple specimens to be

2. Nails - Clean site with 70% ethanol.

Blood - This requires prior laboratory

Thoroughly clean the urethral opening (and

Use sterile tubes or cups to collect and

Use soap rather than disinfectants for cleaning

they can inhibit the growth of microorganisms.

Transport the specimen to the laboratory such that it

inoculate a Thayer Martin plate at the bedside.

and transport to the Laboratory immediately.