SPECIMEN COLLECTION FOR VIRAL INFECTIONS

Please contact the Virus Reference Laboratory, MRI , Colombo.

COLLECTION & TRANSPORT

OF CLINICAL SPECIMENS FOR
MICROBIOLOGICAL INVESTIGATIONS

BLOOD FOR SEROLOGY

A paired sample 7 -14 days apart for a 4 fold antibody rise

A single sample if specific Ig M is to be detected

Collect 5 ml of blood and allow to clot at room temperature.

Separate the serum if possible and send to the laboratory.

Refrigerate if there is a delay.

MICROBIOLOGY LABORATORY
Neville Fernando Teaching Hospital, Malabe

CSF

Collect 2 ml of the sample into a sterile screw capped container

o
Keep at 4 C and send to the laboratory promptly

RESPIRATORY SPECIMENS
For Direct fluorescent antibody test (DFA)

Nasopharyngeal aspirates, Broncho alveolar lavages

Nasal and throat swabs

Collected into viral transport medium (VTM)

Transport VTM packed in ice.

FAECES for Polio and other enteroviruses
Collect 2 samples (8-10 g) within 48 hours
Should be within 14 days of onset of symptoms.
Send to MRI packed in ice.

2014
A report that is issued from a microbiology laboratory is as good as the
specimen that is sent to it. It is important that samples representative of the
infectious disease are collected with care and transported to the laboratory in the
specified manner. The diagnostic procedures and interpretation thus become
more meaningful and useful. Inappropriate samples are a waste of time and
resources and contribute to antimicrobial resistance.

SPECIMENS THAT ARE UNSATISFACTORY AND MAY NOT BE

PROCESSED IN THE MICROBIOLOGY LABORATORY
Urinary catheter tip (a sample of urine when the catheter is removed is
better)
Specimens sent in bottles without screw caps or not supplied by the
lab
Environmental sampling other than in an outbreak
Swabs that appear to be dry.
Urine for culture sent in bottles other than those supplied by
the laboratory
Specimen of saliva instead of sputum (indicated by presence of
epithelial cells)
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Make every effort to obtain specimens prior to the initiation of antimicrobial

therapy.
Use strict aseptic techniques.
Obtain specimens from normally sterile sites, taking care to minimize
contamination by the normal colonizing flora of the skin or mucous
membranes.
Collect an adequate volume of specimen; send tissue or fluid whenever
possible rather than submitting a specimen collected on a swab.
Label all specimen containers with identifying information about the patient
(name, hospital number and ward/unit) and the specimen source and date of
collection.
Fill out all requisitions completely and precisely, including requested details on
patient history, antimicrobial therapy, and specimen source, so that the
laboratory can best determine the appropriate method for processing the
specimen.
Notify the laboratory in advance if special tests are requested or if unusual
pathogens are suspected.
Prompt transport of specimens to the microbiology laboratory is essential in
order to optimize the yield of cultures and the interpretation of results.
Samples for bacterial culture should ideally arrive in the microbiology
laboratory within one to two hours of collection. If a delay is unavoidable,
most specimens (with the exception of blood, CSF, joint fluid, and cultures for
Neisseria gonorrheae) should be refrigerated until transported.
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URINE
Collect an early morning sample of urine.
Container is a sterile, dry, wide mouthed, screw capped bottle
supplied by the lab.
Give clear instructions to the patient to clean the external genitalia
with soap and water, dry and collect urine from the middle of the
stream with as little contamination as possible- MID-STREAM URINE
SAMPLE.
Bed-ridden patients - A Nurse must assist in the cleansing procedure and
collection
Infants and young children
Clean catch specimen- Instruct the mother to clean the external
genitalia of the child and collect urine avoiding contamination when
the child urinates.
Supra pubic aspiration is an alternative procedure to obtain an
uncontaminated sample
Catheterised patients
Do not collect the urine from the urinary bag.
Clamp the catheter for 5-10 minutes. Clean surface of catheter with
antiseptic (70% alcohol). Use a sterile syringe & needle and aspirate
collect urine directly from the catheter.
Transport
The specimens should be sent to the microbiology laboratory within 2
hours of collection, If there is a delay of < 2 hrs.- refrigerate the
specimen at 4oC but should be sent within 8-10 hours in ice.
The time of collection of sample should be indicated on request form
Collection of urine in suspected renal tuberculosis
Early morning sample of urine about 20 ml is collected into a sterile,
dry and leak-proof and sufficiently large bottle, on 3 successive days.
Specimen should be stored at 4oC until all three specimens have been
collected or sent to the laboratory on each day.
Report of culture will be available in 24 hours.
ABST report takes a further 24 hours.

UPPER RESPIRATORY TRACT SPECIMENS

THROAT SWAB
Ideally, specimens should be collected by a physician or other trained personnel.
The patient should sit facing a light source. The tongue is depressed, a sterile
cotton swab is rubbed vigorously over the tonsils, posterior pharyngeal wall &
any other inflamed area. Do not touch the tongue or buccal surfaces. Replace
swab in its container and deliver to laboratory.
Swabs should be taken prior to antibiotics or antiseptic mouthwashes.
It is dangerous to swab the throat of a child with ACUTE EPIGLOTITIS because
it may lead to spasm & obstruct the airway. Instead blood culture should be
done.
NASOPHARYNGEAL ASPIRATES
Gently pass a sterile small-bore catheter through one nostril as far as the
nasopharynx. Attach a sterile syringe to the catheter and aspirate a specimen
of muco-purulent material.
PERNASAL SWAB - for suspected cases of whooping cough
A sterile cotton or alginate wool swab attached to a flexible piece of wire is used.
Gently pass the swab along the floor of the nostril directing it downwards and
backwards as far as the nasopharynx. Replace the swab in its container and
deliver immediately to laboratory. (cough plates are not used as they are
considered a health hazard )
ANTERIOR NASAL SWAB -- TO DETECT S. aureus CARRIERS.
Using sterile cotton wool swab moistened with saline, swab the inside surface of
the nose. Replace swab in its container and deliver to laboratory within 2 hrs.
EAR DISCHARGE
Whenever possible collect or aspirate small amount of discharge into sterile leakproof container. If this is not possible collect specimen onto a sterile cotton wool
swab.
Report of culture - 24 to 48 hours
ABST - 48 hours

BLOOD FOR CULTURE

Take before anti microbial treatment
Take a minimum of two samples of blood (ideally three), within an
interval of 2 hours and from different sites.
(Multiple samples reduce the chance of missing an intermittent bacteriaemia
and helps to determine the pathogenic role of commensal flora)
Volume of blood to be collected from the patient will depend on the
blood culture system used in a hospital laboratory. Blood culture bottles
supplied by the laboratory will indicate the volume of blood to be
collected. Blood should be diluted 5 to 10 times its' volume in broth in
order to prevent clotting, dilute any antibiotic present and minimise the
bactericidal action of human serum.

TECHNIQUE
Skin preparation and venupuncture
Clean the skin of the venepuncture site with tincture of iodine or 10% povidone
iodine followed by 70% alcohol. Allow to dry. Do not touch the site. Wear sterile
gloves and using a disposable syringe and a needle draw the required volume. In
neonates and others when it is difficult to get an adequate volume, do not
attempt to squeeze blood off the vein as this will invariably lead to
contamination by skin flora. Instead inject whatever volume that has been drawn
in to the bottle
o Collect 8-10 ml of blood from an adult patient when bottles supplied by
NFTH laboratory are used.
o Special bottles are available for paediatric patients. Collect 1-3 ml of
blood from children.
Inoculation of blood culture bottles
Remove the metal piece on lid and clean the underlying rubber with 70%
alcohol. Insert the needle through the rubber to pierce it and dispense the blood.
Mix well by rotating the bottle between the palms of your hands or by gentle
inversion.
If samples are collected when the lab is closed, keep bottles at room
temperature. Do not refrigerate.
Preliminary report - 24 hours ( day 2)
nd
2 report ----------- 72 hours ( day 3 or 4)
rd
3 report------------ day 7
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FAECAL SPECIMENS
1. Faeces
Request the patient to pass faeces into a clean, disinfectant free, wide
mouthed container (e.g. bedpan). Faeces should not be contaminated
with urine.
Transfer about a spoonful (containing mucus, pus, blood) of faeces into
a clean (preferably sterile), dry, disinfectant free, leak proof (screwcapped) container.
2. Rectal swabs
A specimen of faeces is always better than a rectal swab.
Use a sterile cotton wool swab moistened with sterile saline or
transport medium. Insert the swab into the rectum, rotate and leave for
about 10 secs., and withdraw.
If the swab could be processed within 2 hrs of collection replace the
swab in the test tube. If it is to be kept for longer than 2 hrs. it should
be inoculated into a transport medium .
3. Transport within 2 hours.
Refrigerate the specimen until despatch to the lab. (If amoebic
dysentery is suspected, a very fresh specimen of faces should be sent).
4. Transport medium. (delay > 2 hours)
Some recommended transport media:
4.1 Carey-Blair medium
Salmonella, Shigella may survive up to 48 hrs; Campylobacter for about
6 hours. Insert a faecal swab into this semi solid transport medium,
brake off the swab stick jutting out of the bottle and replace the bottle
cap tightly.
4.2 Alkaline peptone water or Venkatraman-Ramakrishnan medium
If Cholera is suspected. Transfer about 1 ml of stool into 10 ml of
medium.
Report of culture - 48 hours
ABST - a further 24 hours

CEREBROSPINAL FLUID
Strict aseptic precautions must be adhered to:
Prevent organisms being introduced in to the central nervous system.
Prevent contamination of the CSF specimen which is sterile.
Collect before administration of antibiotics. If patient is already on
antibiotics, indicate on the request form.
Disinfect the skin with iodine / povidone iodine followed by 70% alcohol.
Collect C.S.F. into 3 screw capped bottles for:
Sugar (bottle with Fluoride)
Proteins, cells and Chlorides
Culture & A.B.S.T (sterile, screw capped container
Send to laboratory immediately because delay in examining C.S.F leads to
disintegration of cells & also reduce chances of isolating a pathogen.
If there is a delay keep at room temperature or 37oC.

DO NOT REFRIGERATE

SPECIMENS FROM WOUNDS, ABSCESSES, BURNS, SINUSES

The specimen should not be contaminated with commensal organisms from

the skin.
Collect before applying an antiseptic
Pus from an abscess, vesicles or pustules can be aspirated with a sterile
needle and syringe and transported in the syringe itself or collected into a
sterile, dry, leak-proof container at the time the abscess is incised and
drained, or after it ruptures.
If pus cannot be aspirated, a sterile cotton wool swab can be used to collect
sample of the discharge .
If there is no discharge use a swab moistened with sterile normal saline to
collect the specimen from the edges and depth of the ulcer, thoroughly
rubbing against adjacent healthy tissue.
Segments of tissue from the wound or abscess wall are good specimens
Specimens obtained at surgery from depths of wound or underlying bone
lesions, curettings and tissue biopsies sent in sterile, containers are
excellent
specimens.
If anaerobic infection is suspected, check with the laboratory whether
anaerobic culture is possible and collect the appropriate specimens.

Report of Gram stain - may be available the same day or next day
Report of culture - in 24 or 48 hours
ABST - further 24 hours

SPUTUM
Request the patient to cough deeply to produce a sputum specimen. The
specimen must be expectorated sputum and not saliva and collected early in
the morning into a sterile, wide mouthed, screw capped bottle.
In a child gastric washings can be used for the isolation of M. tuberculosis only
If S. pneumoniae or H. influenzae is suspected transport specimen to the
lab as soon as possble. Do not refrigerate the specimen.
For diagnosis of TB, send 3 early morning sputum samples on consecutive
days for microscopy (AFB) and culture. For isolation of M. tuberculosis specimen
should reach laboratory within 2 hours or should be kept at 4 oC .

Collection of specimen from a mycetoma

Using a sterile hypodermic needle lift up the crusty surface over a sinus
opening. Aspirate discharge if any or insert a ribbon gauze into the sinus
tract, leave for a time and send the gauze in a sterile container to lab.
Report of culture - in 24 to 48 hours
ABST - 48 hours

Report of Gram stain- same day or next day. (The presence of epithelial cells
indicates that it is an unsatisfactory specimen )
Report of culture (other than for M.tb)- after 24 hours
ABST - A further 24 hours
Culture for M. tuberculosis - 8 weeks
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