Complex Characteristics of Yersinia pestis Strains Isolated in the Sarydzhaz and Upper-Naryn High-Mountain Foci in 2019–2020

The aim of the study was a comprehensive analysis of the phenotypic and genetic properties of Yersinia pestis strains isolated in the Sarydzhaz and Upper-Naryn high-mountain foci of the Tien Shan in 2019–2020; determination of the present-day population structure and areal of these highly virulent strains of the plague pathogen.

Materials and methods. Studies of biochemical properties (fermentation of carbohydrates, nutritional requirements), virulence (in vitro and in laboratory animals), molecular-genetic analysis and whole genome sequencing of Y. pestis strains isolated in the Sarydzhaz and Upper-Naryn high-mountain foci in 2019–2020 have been carried out. We used Y. pestis strains from the foci of the Tien Shan and Pamir-Alai dated 1928–2016 for the comparison. Whole genome sequencing was performed using the Ion S5 XL System. Phylogenetic analysis was performed on the basis of 1443 identified core SNPs in 36 Y. pestis strains of various phylogenetic lines included in the analysis. The construction of dendrograms was carried out using the Maximum Likelihood algorithm, PHYML program, HKY85 model.

Results and discussion. It is established that all Y. pestis strains isolated in the Sarydzhaz and Upper-Naryn high-mountain foci in 2019–2020 belong to the 0.ANT5 phylogenetic branch of the ancient biovar of the main subspecies. Genome-wide sequencing revealed the presence of two 0.ANT5 clones, the first of which consists of strains from the basin of the river Kooylu in the Sarydzhaz focus, dated 2020. The second powerful clone includes the strains of 2012–2020 isolated in the Sarydzhaz and Upper-Naryn foci. The high virulence of the isolated strains has been shown. It was concluded that further study of the territories of the highmountain foci of the Tien Shan and Pamir-Alai is necessary to establish the current boundaries of the 0.ANT5 areal, as well as to identify the circulation areas of Y. pestis of other phylogenetic lineages. 

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