Molecular characterization of multiple-drug-resistant Mycobacterium tuberculosis isolates from northwestern Russia and analysis of rifampin resistance using RNA/RNA mismatch analysis as compared to the line probe assay and sequencing of the rpoB gene.

This investigation evaluated the potential of RNA/RNA mismatch analysis for the detection of rifampin resistance among 38 multiple-drug-resistant (MDR) isolates of Mycobacterium tuberculosis from northwestern Russia. The results obtained were compared with a commercialized line probe assay and rpoB sequencing, and the genetic diversity of the isolates was also investigated in parallel using spoligotyping and variable number of tandem DNA repeats (VNTR). The mismatch analysis revealed 3 distinct RNA cleavage profiles permitting the subdivision of the strains into mutation groups 1 to 3, the most common being group 1 (28 of 38 isolates) that contained a majority of strains with a TCG531>TTG (Ser->Leu) mutation, followed by group 2 (6 of 38 isolates) characterized by different mutations in the codon CAC526 (His), and group 3 (4 of 38 isolates), all characterized by a GAC516(Asp) mutation. Spoligotyping revealed the Beijing type to be the most prevalent among mismatch group 1 (24 out of 28 strains), suggesting that the most frequent rpoB mutation among the Beijing family in our setting was TCG531 >TTG (Ser->Leu). All the Beijing type isolates were also characterized by a unique VNTR pattern made up of exact tandem repeats (ETR)-A to E of 42435. We conclude that the Beijing genotype constitutes the major family of MDR-TB isolates currently circulating in northwestern Russia, and that the in-house RNA/RNA mismatch analysis may be successfully used for rapid and reliable diagnosis of rifampin-resistant tuberculosis in this setting.