Genetic diversity of Mycobacterium tuberculosis isolates in the Republic of Sakha (Yakutia), Russia

The population structure of Mycobacterium tuberculosis from Republic of Sakha (Yakutia) was studied using 24-loci MIRU-VNTR genotyping. Most of the studied 199 strains isolated from 199 pulmonary tuberculosis patients (34.2% or 68 of 199 strains) belonged to the Beijing genotype. Multiple drug resistant and extensively drug resistant (MDR/XDR) isolates were predominant (χ² = 15.5; p < 0.001) among representatives of the CC2/W148 subtype of the Beijing genotype (9.5% or 19 of 199 isolates). Strains of the genotype S (15.6% or 31 of 199 isolates) were the second most common genotype after Beijing. Most of the strains of S genotype had an identical profile, 233325153325141344222372. Among non-Beijing isolates, representatives of the S genotype included the most significant proportion of MDR or XDR ((χ² = 59.8; p < 0.001). Isolates of Ural genotype were the third most common (10% or 20 of 199 isolates). The strains belonging to LAM genotype (8.5% or 17 of 199) were genetically heterogeneous. Minor genotypes T and Haarlem were also highly heterogeneous. The epidemic spread of MBT isolates belonging to S genotype and CC2/W148 of the Beijing genotype in Yakutia was reconstructed based on a phylogenetic model. The probable time of origin was estimated using the scale proposed by M. Merker et al. (2015). It was shown that isolates of the CC2/W148 subtype divided into four phylogenetic sublineages and were introduced in the recent historical period (the 20th century). Phylogenetic relationships between 30 MIRU-VNTR profiles of S genotype representatives from Yakutia and 31 reference S-profiles profiles from Europe and Canada were studied. Profiles of the isolates of S-genotype from Yakutia formed compact phylogenetic group. It suggested that these strains have been evolving in Yakutia. It was revealed that the ancestral genotype S was imported onto the territory of Yakutia 300–600 years ago.