Differentiation of Yersinia pseudotuberculosis, Yersinia pestis subsp pestis and subsp microti strains and other representatives of Yersinia pseudotuberculosis complex

Species Yersinia pestis includes two subspecies, pestis and microti. Strains of subsp. pestis were the cause of three plague pandemics. Strains of subsp. microti circulate in populations of rodents belonging to the genus Microtus and cause only rare endemic diseases in human beings that are not accompanied by human-to-human transmission. The existence of combined plague foci with strains from different genotypes, biovars, and even both the Y. pestis subspecies circulating in the same area, as well as periodic introductions of Y. pestis subsp. pestis strains into the foci from which only the strains of subsp. microti were isolated previously, require fast and reliable identification of strain subspecies for optimization of plague prevention and control. For differentiation of Y. pestis subspecies among themselves and against Y. pseudotuberculosis, we analyzed the DNA targets (YPDSF_3711 and opgG), selected the primers, and determined optimal concentrations of the components of the reaction mixture and temperature conditions of PCR. The suggested method allows identification according to the amplicon number and size of Y. pestis subsp. pestis (563 bp), two phylogenetic groups of subsp. microti (SNP-types 0.PE2, 0.PE3, 0.PE4, and 0.PE5, 583 and 426 bp; 0.PE7, 779, 515, and 358 bp), the progenitor of the plague microbe Y. pseudotuberculosis (779, 583, and 426 bp) and Y. similis (779 and 426 bp). The study was carried out on a representative set of strains from the State Research Center for Applied Microbiology and Biotechnology (http://obolensk.org/center/state-collection.htm) and nucleotide sequences deposited in the DDBJ/EMBL/GenBank. The study showed 100% specificity and sensitivity of the proposed method.