Clinical Microbiology In the Department of Pathology

Tuberculosis myositis.  M. tuberculosis is rapidly and accurately detected from fresh and  formalin-fixed  tissue by IS6110 and 16S rRNA real-time PCR.


Direct microscopic exam with fluorescent stain is performed routinely.  A STAT (approximately 2 hour turnaround time) AFB stain is available for initial sputum from patients with suspected untreated tuberculosis, however this process renders the specimen unsuitable for other studies and additional samples must be submitted for culture.

Direct detection of Mycobacterium tuberculosis using real-time PCR:
Real-time PCR for detection of M. tuberculosis complex is automatically performed on smear-positive respiratory specimens.  Smear-negative specimens are tested by request.  Genotypic susceptibility testing for rifampin and isoniazid as well as fluoroquinolone and injectable drugs are performed by request at California Department of Public Health, Microbial Diseases Laboratory.

Culture and identification of mycobacteria using broth and plates:
Microbiology uses Middlebrook plates and an automated broth incubation system for detection of mycobacterial cultures.  Positive isolates are identified with multiplexed, real-time PCR and ribosomal RNA gene sequencing.  Mycobacterium tuberculosis complex and Mycobacterium chelonae-abscessus group are further identified to species level.  Aerobic actinomycetes, Nocardia species in particular, are identified by ribosomal RNA gene sequencing.

Antibiotic susceptibility testing:
M. tuberculosis complex isolates are tested for sensitivity to first-line drugs with the MGIT instrument.  Second-line testing is performed at reference laboratories.  M. avium complex are tested against clarithromycin using a broth microdilution method.  Rapidly growing mycobacteria and other aerobic actinomycetes are tested with antibiotic-impregnated strip method.

Latent tuberculosis infection testing:
Past exposure to M. tuberculosis is detected using a whole blood interferon-gamma release assay (IGRA).  The laboratory has extensive experience with IGRA and has conducted investigations to measure the performance of this assay.

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