Diagnosis of pulmonary tuberculosis in a microbiological laboratory.

The positive diagnosis of pulmonary tuberculosis still relies on the direct detection of Mycobacterium tuberculosis complex strains after isolation, culture, and identification, or on the detection of specific DNA sequences. Clinical specimens for the direct diagnosis include respiratory tract and stool specimens, which can all be collected with a "tuberculosis kit" to simplify and standardize clinical and laboratory tasks. Gastric juice and other specimens are no longer useful. The association of new decontamination technics, new liquid and solid Middlebrook blood-enriched culture media allow for the isolation of tuberculous mycobacteria in 10 days. The microscopic-observation drug susceptibility and thin layer agar assays allow for rapid detection of M. tuberculosis including drug-resistant tuberculosis. "Closed molecular tests" adapted to "point-of-care" use allow for the detection of tuberculous mycobacteria in Ziehl-positive samples and the detection of rifampicin resistance in three hours. Rapid identification can be achieved with protein spectrum analysis by mass spectrometry. Finally, genotyping by various technics of profile analysis (spoligotyping, VNTR-MIRU) or by sequence analysis (multispacer sequence typing) allows for the identification of isolates among the six Mycobacterium tuberculosis complex species, and for the detection of laboratory cross-contaminations. It also allows diagnosing cross-transmission between patients including nosocomial cases, discriminating between reactivation and new infection, and determining the geographical origin of strains (geotyping). The ongoing search for new culture media is a priority to improve the speed of direct diagnosis of pulmonary tuberculosis.