PREVALENCE AND DIVERSITY OF NONTUBERCULOUS MYCOBACTERIA IN DIFFERENT REGIONS OF THE RUSSIAN FEDERATION

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Evaluation of hybridisation on oligonucleotide microarrays for analysis of drug-resistant Mycobacterium tuberculosis

A molecular approach was developed to identify drug-resistant strains of Mycobacterium tuberculosis by means of biochips with oligonucleotides immobilised in polyacrylamide gel pads. The technique was based on multiplex PCR, followed by hybridisation on an oligonucleotide microarray, and detected > 95% of rifampicin-resistant and c. 80% of isoniazid-resistant M. tuberculosis isolates within 12 h. In total, 220 drug-resistant isolates and 131 clinical samples were tested using biochips. The sensitivity and specificity of the developed method were comparable with those of standard bacteriological testing of M. tuberculosis drug resistance.

[Spoligotyping of mycobacterium tuberculosis isolates obtained from patients in the Samara region]

The spoligotyping of 138 M. tuberculosis isolates obtained on the territory of the Samara region made it possible to classify them as belonging to 27 groups. The largest cluster including 94 strains (68.1%) belonged to Peking spoligotype. As shown with the use of the commercial system INNO-LiPA, 78 out of 134 strains (58.2%) had mutations in different sites of gene pro B. The analysis of the markers of resistance to rifampicin in Peking spoligotype revealed that 65 (83.9%) out of 90 such cultures had mutations in gene pro B, i.e. potentially these strains had multiple antimicrobial resistance. This work demonstrated the prevalence of Peking spoligotype in a prison antituberculosis colony (81.6%).

[Typing of Mycobacterium tuberculosis cultures from Samara region by the variable number of tandem repeats]

To type Mycobacterium tuberculosis (MT) strains by the variable number of tandem repeats (VNTR), 136 MT cultures, isolated in 5 main general therapeutic laboratories and penitentiary antituberculosis institutions of the Samara region, were studied. Gene typing revealed that the greatest number of MT strains (73) belonged to VNTR type 42435. It was followed by VNTR type 22232, found in 13 isolated cultures. Among the MT cultures of the most widely spread VNTR type 42435, rifampicin-resistant strains prevailed (57 strains, i.e. 78%), while strains belonging to VNTR type 22232 were mainly sensitive to rifampicin (84%). VNTR typing of MT typing may be useful for epidemiological studies in the field of phthisiology.

Identification of rifampin-resistant Mycobacterium tuberculosis strains by hybridization, PCR, and ligase detection reaction on oligonucleotide microchips

Three new molecular approaches were developed to identify drug-resistant strains of Mycobacterium tuberculosis using biochips with oligonucleotides immobilized in polyacrylamide gel pads. These approaches are significantly faster than traditional bacteriological methods. All three approaches-hybridization, PCR, and ligase detection reaction--were designed to analyze an 81-bp fragment of the gene rpoB encoding the beta-subunit of RNA polymerase, where most known mutations of rifampin resistance are located. The call set for hybridization analysis consisted of 42 immobilized oligonucleotides and enabled us to identify 30 mutant variants of the rpoB gene within 24 h. These variants are found in 95% of all mutants whose rifampin resistance is caused by mutations in the 81-bp fragment. Using the second approach, allele-specific on-chip PCR, it was possible to directly identify mutations in clinical samples within 1.5 h. The third approach, on-chip ligase detection reaction, was sensitive enough to reveal rifampin-resistant strains in a model mixture containing 1% of resistant and 99% of susceptible bacteria. This level of sensitivity is comparable to that from the determination of M. tuberculosis drug resistance by using standard bacteriological tests.