Efficiency of Different VNTR Loci in the MLVA25 Analysis of Yersinia pestis Strains of Medieval Biovar from Eastern Europe and Central Asia Foci

Multilocus variable number tandem repeat analysis (MLVA) is one of the highest-resolution methods for subtyping genetically monomorphic pathogens of especially dangerous infections. The MLVA25 method of subtyping based on 25 VNTR loci, which is widely used in molecular epidemiological studies, has shown high efficiency in the analysis of Yersinia pestis strains. However, the question of the efficiency of individual VNTR loci in MLVA25 of Y. pestis strains of medieval biovar of main subspecies prevalent in most natural plague foci of Eastern Europe and Central Asia remains open. The aim of the present work was to evaluate the efficiency of different VNTR loci and to optimize the MLVA25 method for differentiation of Y. pestis strains of medieval biovar from the plague foci of Russia and other CIS countries located in Eastern Europe and Central Asia. Whole genome sequences of 220 strains of Y. pestis of medieval biovar of main subspecies and 31 strain of Y. pestis belonging to other phylogenetic lineages were analyzed. The sequences of VNTR loci identified in these strains were entered into the Bionumerics 7.6.3 software for subsequent phylogenetic analysis by UPGMA. MLVA25 genotypes of 251 Y. pestis strains used in this work were identified. According to the results of the statistical analysis of these loci, 126 individual genotypes were detected in the strains of medieval biovar, which corresponds well with the discrimination ability of the subtyping system (DP = 0.98). Efficient loci with high discrimination power were identified, which have the greatest impact on the differentiation of the strains of medieval biovar by genotype. An MLVA subtyping system for Y. pestis strains of medieval biovar has been optimized, into which 12 VNTR loci were included.