Spatial and Temporal Characteristics of Yersinia pestis Strain Properties in the Natural Plague Foci of Kazakhstan

This study presents a comprehensive analysis of Yersinia pestis (Y. pestis) strains circulating in the natural plague foci of Kazakhstan, based on integrated epizootological monitoring, microbiological, and advanced molecular genetic methods. The research aims to assess the genetic biodiversity of Y. pestis , evaluate the effectiveness of analytical approaches, and develop a structured algorithm for the application of genotyping tools in building a national biorepository of natural isolates. Uniquely, the study combines classical microbiological techniques with high-throughput technologies including PCR, MLVA (VNTR), VITEK 2 Compact, MiniION (Oxford Nanopore), MiSeq (Illumina), and GIS-based spatial mapping. A total of 1,220 Y. pestis strains (2010–2023) were phenotypically and genotypically characterized, revealing that 94.8% were typical for their ecological settings, while 5.2% exhibited deviations. Additionally, whole-genome and multilocus analyses of 82 DNA samples allowed for the construction of three phylogenetic trees and GIS-integrated visualizations, offering new insights into the spatial and temporal dynamics of plague in Central Asia. A genetic repository was established, forming the foundation for future research on the evolution, distribution, and risk of plague in endemic regions. These findings represent the first large-scale genomic profiling of Y. pestis in Kazakhstan and provide essential tools for public health surveillance and biosecurity.