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The paper reports the investigation of the population structure of Yersinia pestis strains belonging to the ulegeica subspecies (genetic branch 0.PE5), which is endemic to the natural plague foci in Mongolia and which is characterized by low epidemic potential compared to the strains belonging to the main plague subspecies. Whole genome SNP analysis of 12 Y. pestis subspecies ulegeica strains isolated in Mongolia considering the 1581 identified core SNPs revealed two main genetic clusters in correspondence with the geographic distribution of these strains. The first cluster, named 0.PE5/1, contains the strains isolated in the Umnegov’, Uverkhangai, and Gov’-Altai aimaks located in the south of Mongolia. The second cluster 0.PE5/2 comprises two subclusters, namely, 0.PE5/2-1, containing the strains from the Bayan-Ulgii and Khovd aimaks, and 0.PE5/2-2, represented solely by the strains isolated in the Bayan-Ulgii aimak. To find the possible causes of the selective virulence of subspecies ulegeica strains, the analysis of the nucleotide sequences of 79 pathogenicity factors along with some other genomic regions has been carried out. Specific mutations have been found in the following genes: irp1, included in the high-pathogenicity island of the chromosomal pigmentation region, and yscQ, involved in the regulation of the synthesis of the LcrV protein and outer membrane proteins (Yops) associated with plague pathogen virulence.

The genetic diversity of Yersinia pestis strains from the Mongolian natural plague foci has been investigated. A total of 32 strains isolated from western, eastern, and central aimaks, as well as from the territory of the Gobi region, have been studied. Twenty-four strains belong to the main Y. pestis subspecies, while eight belong to non-main subspecies. There is only one strain of biovar medievalis (genovariant 2.MED1) among the strains of the main subspecies, while the rest of the subspecies belong to the biovar antiqua. Biovar antiqua strains are split into three groups. Strains from the eastern part of the country were classified as genovariant 2.ANT3, and those from the western and central regions were classified as genovariant 3.ANT2, which was endemic for Mongolia. One strain from the Bayan-Ulegeiskii aimak had the rare genovariant 4.ANT. None of the strains of the biovar antiqua belonged to its ancient 0.ANT branch, which is inconsistent with the commonly accepted idea that ancient marmot’s plague agent race originates from Mongolia. Six out of eight strains of the non-main subspecies belonged to the ulegeica subspecies, which are endemic to Mongolia, one strain belonged to the microtus group, and the last belonged to a previously uncharacterized variant of the minor subspecies.

The results of a study on the taxonomy and quantitative abundance of free-living amoebas in soil samples from the Russian plague foci of the Northwestern Caspian steppe, the Caspian sand, and the Volga-Ural steppe are presented. Amoebas of the Willaertia and Hartmanella genera, as well as representatives of myxomycetes, were isolated from samples. From these, amoebas of the Acanthamoeba genus predominated and could be as abundant as 300000 cells per 1 g of soil. Sequencing of the18S rRNA gene region showed that Acanthamoeba from the Volga-Ural steppe focus belonged to the A. castellanii species. Phylogenetic analysis confirmed that amoebas from two other Caspian foci belonged to the species of Acanthamoeba spp.

The nucleotide sequences of the Tc’s insect toxin complex genes have been analyzed in 18 natural strains of the main and non-main subspecies of Yersinia pestis isolated in different natural foci in the Russian Federation, as well as neighboring and more remote countries, as compared to the data on Y. pestis and Y. pseudotuberculosis strains stored in the NCBI GenBank database. The nucleotide sequences of these genes in plague agent strains have been found to be highly conserved, in contrast to those of the pseudotuberculosis agent. The sequences of two genes, tcaC and tccC2, have been found to be almost identical in Y. pestis strains, whereas other three genes (tcaA, tcaB, and tccC1) contain a few mutations, which, however, are not common for all strains of the plague agent. Exceptions are only strains of the Y. pestis biovar orientalis, whose tcaB gene is in a nonfunctional state due to a nucleotide deletion. The results suggest that the formation of the species Y. pestis as an agent of a natural focal infection with a transmissive mechanism has not resulted in degradation of the Tc’s complex genes. Instead, these genes are likely to have been altered as the plague agent have been adapting to the new environment.