Mycobacterium tuberculosis Beijing genotype in Russia: in search of informative variable-number tandem-repeat loci

Abstract

The Beijing genotype is a globally spread lineage of Mycobacterium tuberculosis. In Russia, these strains constitute half of the local population of M. tuberculosis; they are associated with multidrug resistance and show increased transmissibility. Here, we analyzed traditional and new markers for the rapid and simple genotyping of the Beijing strains. A representative sample of 120 Beijing genotype strains was selected from a local IS6110-restriction fragment length (RFLP) database at the St. Petersburg Pasteur Institute. These strains were subjected to variable-number tandem-repeat (VNTR) typing using 24 loci of a newly proposed format and three hypervariable (HV) loci (QUB-3232, VNTR-3820, and VNTR-4120). Ten of the 27 VNTR loci were monomorphic, while five loci, MIRU26, QUB-26, QUB-3232, VNTR-3820, and VNTR-4120, were the most polymorphic (Hunter Gaston index, >0.5). VNTR typing allowed us to differentiate between two large IS6110-RFLP clusters known to be prevalent across the entire country (clusters B0/W148 and A0) and identified in 27 and 23% of strains, respectively, in the Beijing genotype database. The B0/W148 strains were grouped closely in the VNTR dendrogram and could be distinguished by a characteristic signature of the loci MIRU26 and QUB-26. Consequently, this clinically important IS6110-RFLP variant, B0/W148, likely presents a successful clonal group within the M. tuberculosis Beijing lineage that is widespread in Russia. To conclude, the IS6110-RFLP method and VNTR typing using a reduced set of the most polymorphic loci complement each other for the high-resolution epidemiological typing of the M. tuberculosis Beijing genotype strains circulating in or imported from Russia.

FIG. 1.

Twenty-seven VNTR locus-based UPGMA dendrogram and IS6110-RFLP profiles of the 48 M. tuberculosis Beijing genotype strains (study set 1). IS6110-RFLP profile codes are boxed. The B0 cluster (B0 and B0-like profiles) is shaded and marked by an asterisk.

FIG. 2.

Seventeen VNTR locus-based UPGMA dendrogram of the combined sample of 120 M. tuberculosis Beijing genotype strains. The B0 cluster (B0 and B0-like profiles) is shaded. The asterisk to the left of the VNTR digital profile designates missing data due to PCR failure. The number of strains is shown if it is greater than one.

FIG. 3.

VNTR-based minimum spanning tree of the VNTR types within the B0 cluster. Circle sizes are roughly proportional to the number of strains. VNTR digital profiles are shown in Fig. 2.