Microbiology Specimen Collection
In terms of effectiveness, nothing is more important than the appropriate selection, collection and handling of a
specimen for microbiological analysis.
The appropriate specimen collection and management directly affects patient care in relation to the accurate
laboratory diagnosis, appropriate therapeutic decisions and the duration of patient suffering.
General Collection Guidelines
• Selection of specimen or collection site must represent
the location of active disease.
• Avoid commensal contamination from indigenous flora
where possible, to ensure a sample is representative of
the infectious process
• Collect adequate volumes of sample. Insufficient material
may yield false negative results.
• Use appropriate collection devices and sample
containers.
Sputum
For routine examination specimens should contain purulent
lower respiratory tract secretions with minimal contamination
by saliva. The patient should be asked to take a deep breath
and cough as vigorously as possible, spitting the sputum into
the container. If possible an early morning specimen should be
collected. Patient instruction sheets are available on request.
All specimens must be refrigerated after collection to prevent
overgrowth by contaminants. For mycobacteriology (tb/afb)
requests, early morning sputum from 3 different days are
required. These can be presented to the laboratory at one visit.
Urine Collection
Urines are the most common specimen for microbiological
analysis. They are easily contaminated with the patients own
microflora from urethra or periurethra. A clean catch specimen
is vital to the achievement of meaningful results once the
specimen reaches the laboratory. Urine specimens should be
refrigerated to prevent an overgrowth of possible contaminants.
Faeces Samples
When requesting faecal testing, sterile brown topped
opaque containers are available from the laboratory or your
nearest collection centre. Please emphasise to your patients
that the laboratory only requires a “walnut” sized sample and
that the whole motion is not needed.
• One sample can be utilised for multiple tests e.g. culture,
occult blood and virus testing.
• The specimen should be as fresh as possible and be stored
at 4°c if transport is delayed. In the case of specimens for
reducing substances the sample should be placed on ice if
the delay to the laboratory is 4-6 hours and frozen if more
than 6 hours. If the sample needs to be frozen, a separate
specimen will be needed for culture.
• For occult blood (FOB) testing a fresh sample should
be collected on three consecutive days (if FOB x3 are
requested) and submitted to the laboratory each day.
Urine Collection Guidelines
Name
Abbreviation
Use
Mid Stream Urine
MSU
Collected for bacterial culture, and some biochemical tests. Patient cleans area and passes
the first portion into the toilet. They then collect between 20-40ml in the jar and then pass the
remaining sample into the toilet.
Detailed instructions and collection bags are available from the laboratory for your patients to
assist with this type of collection.
Bag Urine
First Void Urine
Terminal Void
Urine
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FVU
FVU are required for PCR testing for Chlamydia and Gonorrhoea. The first part of the urine
sample (approx 20mL) is critical to the accuracy of this test. If bacterial culture is also required two
samples MSU and FVU should be collected.
The terminal part of the urine stream taken between 10.00am and 2.00pm. 3 samples should be
collected on 3 different days. Used for the detection of schistosoma haematobium.
Male Sex Hormones and Related Disorders continued
Medicare restricts the number of faecal samples
that can be tested and rebated in a given period
Request
Abbreviation
No. of Samples
rebated
Micro Culture
and Sensitivity
M/C/S
1 in 7 day period
Ova, Cysts
and Parasites
O/C/P
2 in 7 day period
Enteric viruses
(Rotavirus, Adenovirus,
Norovirus, enterovirus )
No limit
Reducing Substances
No limit
Occult Blood
FOB
3 in 28 days
• When collecting wound swabs, the advancing margin of the
lesion, (not the centre) will give a more representative picture
of the disease. Specimens should be labelled with the site
of the lesion. Additional information on the request form
including whether the sample is surface or deep and the
lesions history will also aid in diagnosis.
• For throat swabs the tonsillar area should be sampled with
attention given to areas of inflammation and/or exudate.
The gums, teeth and cheeks should be avoided to prevent
contamination with the patients own microflora.
• When collecting nasal swabs, the swab should be
moistened using sterile saline (or the gel in the transport
tube) and inserted at least 1cm inside the nares, rotating the
swab against the nostril wall.
Swabs for culture should be stored at room temperature.
Swab Collection
Swab for PCR testing
Swab for Culture (Bacterial)
When collecting swabs for culture it is important that
the collection site represents the location of active disease.
Specimens that require culture need to be collected using
blue topped swabs and placed into transport medium.
Specimen collected in transport medium (Blue top)
cannot be used for PCR.
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Specimens that require PCR testing must be collected using
orange topped swabs and placed into empty plastic tubes
with NO transport medium. Common tests requested for PCR
include N.gonorrhoea, Chlamydia, Ureaplasma/Mycoplasma
Herpes I/II, Influenza, adenovirus, Enterovirus, Bordetella.
Note: Orange top (dry) swabs are unsuitable for microscopy,
culture and sensitivity.
Additional guidance for microbiology sample collection can
be obtained from our web site, www.clinipathpathology.
com.au or by contacting Mr Kevin Mcleod, our senior
scientist in microbiology on 9476 5233.