Background. The Latin American–Mediterranean (LAM) genotype of Myobacterium tuberculosis is widespread in most regions of the world. Its LAM-RUS branch is endemic to Russia and Northern Eurasia and is frequently multidrug-resistant. Although geographically distant, the LAM-RUS strains are closely related in their 24-MIRU-VNTR profiles, which may reflect their relatively recent dissemination across this sparsely populated area of Northern Eurasia. Practically, this means that the international 24-locus MIRU-VNTR format has limited utility for subtyping LAM-RUS strains. Here, we evaluated seven additional hypervariable VNTR loci for their discriminatory power among LAM-RUS strains.
Methods. A sample of 133 M. tuberculosis LAM strains from different locations was subjected to spoligotyping (followed by comparison with the SITVIT2 database) and 24-locus MIRU-VNTR typing. Seven hypervariable VNTR loci (3820, 4120, 3232, 1982, 2136a, 3155, and 3336) were additionally genotyped. MIRU-VNTRplus.org and PAUP software were used for the phylogenetic analysis of the VNTR data, treated as discrete variables. The Hunter–Gaston Index (HGI) was used to assess the discriminatory power of individual loci and their combinations.
Results. Based on spoligotyping, 22 different spoligotypes were identified, of which SIT42 was the most prevalent (n=37), followed by SIT254 (n=26) and SIT252 (n=22). Thirty-locus typing revealed 14 clusters (2–15 isolates) and 58 unique profiles. The Hunter–Gaston Index (HGI) for the 30-locus set was 0.979. The HGI values for individual loci ranged from 0 (MIRU4, MIRU24, MIRU39, Mtub29) to 0.5595 (VNTR3820) and 0.6165 (MIRU40). The combined discriminatory power of the 11 most polymorphic loci was 0.968 (13 clusters of 2–17 isolates; 67 unique profiles), which was nearly equivalent to that of the full 30-locus VNTR set.
Conclusions. This optimized 11-locus panel provides sufficient discriminatory power for LAM genotype strains and could serve as a cost-effective tool for primary epidemiological surveillance of this clinically important M. tuberculosis lineage.
