Molecular Identification of Yersinia pestis Strains Isolated in the Aksai High-Mountain Focus of the Kyrgyz Republic in 2024

The Aksai high-mountain focus is part of the Tien Shan focus, which has recently shown constant epizootic activity. In 2024, Yersinia pestis cultures were isolated from the Aksai focus for the first time in the 21st century. The aim of the study was molecular identification of Y. pestis strains collected in the Aksai focus in 2024, their phylogenetic analysis to establish their origin and obtain whole-genome sequences that are reference ones for this focus in the mo dern period. Materials and methods. The genomes of Y. pestis strains were sequenced on a MinIon genetic analyzer (Oxford Nanopore Technologies, UK). Sequencing libraries were prepared using the Native Barcoding Kit 24 v14 (SQKNBD114.24) and sequenced on an R10.4.1 flow cell. Core SNPs were identified applying pair wise alignment of the obtained whole-genome sequences to the genome of Y. pestis CO92 strain using Snippy v4.6.0 software. The Maximum Likelihood dendrogram was constructed using PhyML 3.1. Results and discussion. According to the phylogenetic analysis of whole-genome sequences, it has been established that the Y. pestis strains isolated in the Aksai focus in 2024 belong to the phylogenetic branch 0.ANT3 of antique biovar. The Y. pestis strains of 2024 fall under the 0.ANT3 polytomy, which also includes all 0.ANT3 strains of the 20th century from the Aksai, Upper Naryn and Alai high-mountain foci and strains from the Xinjiang province in China. The genetic differences between the 0.ANT3 strains of the current and last centuries are small, which proves the continuity of the preservation of this population in the 20th–21st centuries and the local origin of the 2024-strains. Strains 0.ANT3 were previously isolated across large areas of the Upper Naryn, Aksai, Alai plague foci and on the adjacent territories of China, which indicates the existence of a mega-focus of 0.ANT3 Y. pestis there. Strains 0.ANT3 are highly virulent and epidemically significant. The activation of the Aksai natural plague focus requires increased epidemiological surveillance of this autonomous plague focus in the Tien Shan.

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