Phylogeographic Analysis of Yersinia pestis Subspecies ulegeica Strains

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.