Specimen Collection
Sputum (Expectorated / Induced)
Collect one specimen a day for three successive days into wide mouthed leak proof containers.
Body fluids
Pleural, pericardial and other body fluids: minimum of 5-10 mL to be collected into citrate tube.
Rejected
: EDTA specimens
Tissue
Small biopsy material should be placed in sterile saline or distilled water. Larger specimens in sterile pot with no additives.
Rejected
: Specimens in 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*.
* Myco-F-Lytic bottle: Please request these bottles from the Microbiology laboratory (Ext 22706).
Urines
Three early morning specimens (first catch) in TB gastric/urine bottles* on two to three consecutive days. Please collect 50mL volume.
Only mycobacterial culture will be performed on appropriate urine specimens. TB smear and PCR is not performed on these specimens.
Rejected
: 24-hour urine or midstream urines will be not be processed.
* TB gastric/urine bottles: Please request these bottles from the Microbiology laboratory (Ext 22706).
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.
* TB gastric/urine bottles: Please request these bottles from the Microbiology laboratory (Ext 22706).
Bone marrow
Inoculate 1-5mL sample directly into sterile Myco-F-Lytic bottle*.
Rejected
: EDTA specimens
* Myco-F-Lytic bottle: Please request these bottles from the Microbiology laboratory (Ext 22706).
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 10:00 hours (Monday to Friday) for the smear result to be available on the same day.
Positive cultures of acid-fast bacilli are reported immediately after growth occurs. Negative culture results are reported after completion of 6 weeks incubation time.
-
Smear results are available within 24 hours of specimen arrival at the TB laboratory (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 (0.1 ug/mL and 0.4 ug/mL), Rifampicin and Ethambutol. Moxifloxacin is included in the first line panel.
Results are usually available within 3 weeks of a confirmed culture.
Second Line Drugs
: Amikacin, Bedaquiline, Ethionamide, Linezolid and Moxifloxacin.
Pyrazinamide phenotypic susceptibility testing is currently not available due to manufacturer technical issue.
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
Transportation:
Respiratory specimens for TB examination should be transported chilled (2-8 deg C).
Cultured isolates
Referred Mycobacterium
cultures
must be sent at ambient temperature and under required IATA UN2814 (Infectious substances) regulations.