Specimen Collection
Sputum (Expectorated / Induced)
Collect one specimen a day for three successive days into wide mouthed leak proof containers.
Body fluids
Pleural and other body fluids to be collected into citrate bottle.
Tissue
Small biopsy material should be placed in sterile saline or distilled water. Larger specimens in sterile pot with no additives. Do not use formalin.
Pus
Aspirates or pus swabs should be sent in a sterile container.
Blood culture
Collect a maximum of 5 mL into Myco-F-Lytic blood culture bottles. Please request these bottles from the laboratory.
Urines
Three early morning specimens in TB gastric - urine bottles (an adequate specimen of 60 mL must be sent). A 24 urine hour specimen will not be processed.
Gastric washings
Early morning fasting specimen in TB gastric - urine bottle, collected before the patient rises. The total gastric contents are required in the special gastric/urine bottles. These bottles contain bicarbonate to neutralise the acidity of the specimen. Mycobacteria become nonviable in an acid medium.
Bone marrow
Cultured at time of collection (maximum 5 mL) into Myco-F-Lytic blood culture bottles. Please request these bottles from the laboratory.
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.
Atypical Mycobacteria/MAIC organisms
Collection of specimens is as above.
Turnaround Time:
Specimens must reach the laboratory before 1000 hours for the smear result to be available on the same day.
Positive cultures of acid-fast bacilli are reported immediately growth occurs (minimum 4 days), while negative culture results will not be available for 6 weeks.
Please telephone the laboratory before sending an urgent specimen.
-
Smear results are available within 24 hours of specimen collection (Monday-Friday)
-
Culture and identification results are available for new smear positive cases within 14 days
-
Susceptibility testing will be available within 15-30 days for smear positive cases
-
Referred cultures of
Mycobacterium tuberculosis
should have susceptibility results reported within 28 days
Diagnostic Use and Interpretation
Culture identification
A Tb antigen test to confirm or exclude
Mycobacterium tuberculosis
is performed on all new cultures. A DNA probe to identify
M. avium
complex is performed as required. Identification of significant non-tuberculosis mycobacteria may take up to two weeks.
Drug susceptibility
-
First Line Drugs
: Isoniazid, Rifampicin, and Ethambutol. Results are usually available within 7 days of a confirmed culture. Pyrazinamide results are available within 3 weeks.
-
Second Line Drugs:
Rifabutin, Ethionamide, Moxifloxacin, Bedaquiline, Clofazimine,Linezolid and Amikacin. Available for drug resistant Tb. Please consult with the laboratory.
Note
: Clarithromycin is the only drug tested against
M. avium
complex.
Also see:
Mycobacterium avium complex PCR
Mycobacterium tuberculosis PCR
QuantiFERON-TB Gold
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
Specimen Transport Instructions for Referring Laboratories
Specimens and referred cultures must have at least
two identification points
, preferably name and NHI number.
Specimens
Specimens for example sputum, are to be transported chilled.
Cultured isolates
Referred Mycobacterium
cultures
must be sent at ambient temperature and under required IATA UN2814 (Infectious substances) regulations.