Specimen Collection
Full clinical details are essential
. This enables the laboratory to select appropriate tests and request additional specimens where necessary to establish the diagnosis. Additional consultation may be indicated. Please discuss if urgent or non-routine specimens are being sent.
NOTE: DO NOT USE HEPARIN TUBES for any DNA analysis
CSF
10-20 ml of CSF is recommended for the investigation of M. tuberculosis meningitis (in adults). Collect in sterile CSF tubes. Specimens of sufficient volume will undergo mycobacterial culture and MTB PCR (GeneXpert MTB/RIF assay). Specimens with a normal white cell count or inadequate volume will not be routinely processed.
Fresh tissue biopsy
Keep moist with saline. Do not submit on paper. These are preferable to paraffin-embedded specimens.
Pleural fluid / pericardial fluid
Minimum of 5 - 10 mL collected into a citrate or an EDTA or CPD tube.
Bone Marrow
Collect into an EDTA or CPD tube
FNA
Collect into a sterile container.
Sputum
Sputum is processed on Xpert MTB/RIF real-time PCR.
Swab
PCR is not routinely performed on swabs of any kind.
Paraffin block shavings
MUST be sent in a sterile container with minimum of 12 shavings (10-20 microns)
DO NOT SEND THE BLOCK
Turnaround Time:
This test is performed in a weekly batch.
Specimens received in the Microbiology laboratory
before 1000 hrs on Monday
will be processed that day and the results available on Tuesday.
Specimens arriving
after 1000 hrs on Monday
will be held and processed in the following Monday's batch.
Turnaround time excludes weekends and public holidays.
Please discuss with the Clinical Microbiologist if urgent or non-routine specimens.
Hours of service:
Monday to Friday only.
Diagnostic Use and Interpretation
Results
PCR detects MTB complex (which includes M.tuberculosis and M.bovis)
IMPORTANT NOTE - Please read:
Because of the difficulty in defining a "gold standard" of diagnosis for tuberculosis in many cases, the sensitivity and specificity of PCR for each specimen type has not been validated and will depend on a number of factors, including volume of specimen. However, local experience with the test suggests sensitivity to be about 50%, whereas overall specificity is 95% or more when compared to clinical diagnosis and culture.
PCR for M tuberculosis DNA will have most value when the possibility of infection is high and much less if used as a "screening test". The value of the test performed on CSF with < 5 white blood cells is very doubtful and requires prior discussion with a clinical microbiologist (see below).
It is essential that microscopy and culture for mycobacteria also be requested as PCR-negative, culture-positive results may be obtained. In addition, culture will allow susceptibility tests to be performed.
A positive PCR result for M. tuberculosis is highly significant; a negative PCR result does not exclude infection.
Also see:
Tuberculous specimens
Contact Information
For further information, contact the Microbiology Department via Lablink or the Clinical Microbiologist:
Lablink contact details
Dr Sally Roberts
, Microbiologist:
ext 22705
Cellphone
021 674 140
Dr Sharmini Muttaiyah
, Microbiologist:
ext 22700
Cellphone
021 615 892
Dr Mary de Almeida
, Microbiologist:
ext 22700
Cellphone
021 170 9117
Dr Matthew Blakiston
, Microbiologist: contact via Lablink