Mycobacteria testing


Sputum (3-5 separate samples);

bronchoscopy brushing, lavage;

tissue biopsy (eg, lymph node, lung, endometrial curettings, bone);

body fluids (eg, CSF, pleural, synovial, pericardial fluids);

pus (swabs do not provide an adequate sample);

urine (3 complete early morning collections);

blood culture collected into specialized culture medium;

bone marrow aspirate;


tissue fluid from eg, eyebrows, ear lobes.


Acid fast staining (eg, Ziehl-Neelsen) or auramine staining for microscopy;

gene probe following PCR amplification for some specimens (eg, CSF);

culture in/on appropriate media (eg, Lowenstein-Jensen or Middlebrook).

Rapid growers (eg, M. fortuitum) may grow in 1-2 weeks, but 6-8 weeks of incubation are required before discarding negative cultures.

Identification of mycobacteria and antibiotic susceptibility testing take another 4 weeks using conventional techniques.

The use of culture systems using liquid media combined with gene probe (for identification) considerably reduces the time required for testing.


Suspected tuberculosis or atypical mycobacterial infection, including unexplained lung infection;

'sterile' pyuria;


diarrhoea or fever in patients who have AIDS;

chronic skin ulcers/lesions;

subacute/chronic unexplained lymph adenopathy;

infertility (endometrial curettings);

suspected leprosy (microscopy of tissue fluid from eyebrows, ear lobes, skin, or biopsy).

Biopsy of tissue has higher sensitivity than fluid samples.


The presence of acid fast bacilli in sputum or in normally sterile fluids or tissues is generally sufficient to establish the diagnosis of tuberculosis in the context of a typical clinical presentation.

However, the sensitivity of microscopy in body fluids and CSF is low (<20%).

NAA allows more rapid detection and differentiation of Mycobacterium tuberculosis from other mycobacteria; culture confirms the diagnosis and allows identification of non-tuberculous mycobacteria and antibiotic susceptibility testing.

M. leprae cannot be grown in vitro and the diagnosis of leprosy is based on the presence of acid fast bacilli in a clinically suspicious lesion or NAA detection.


Pfyffer GE et al. In: Murray PR et al eds. Manual of Clinical Microbiology. 8th Ed.2003. ASM Press.

Hale YM  et al. Clin Infect Dis. 2001; 33: 834-846.

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