Spatial and temporal characterisation of genetic and phenotypic properties of Yersinia pestis in Kazakhstan’s natural plague foci

The study aimed to analyse data from epizootological monitoring, microbiological and molecular genetic studies to assess the genetic biodiversity of Yersinia pestis (Y. pestis) strains, to determine the effectiveness of using individual methods and to develop the necessary algorithm for evaluating genetic methods and creating a biorepository of natural isolates of these pathogens. As a result, the biodiversity of Y. pestis strains isolated in natural plague foci of Kazakhstan was analysed using classical and modern methods (polymerase chain reaction, Multi Locus Variable Number Tandem Repeat Analysis, VITEK 2 Compact, MiniION Oxford Nanopore, MiSeq sequencer) of research and geographic information system (GIS) technology. Spatial and temporal characteristics of plague infection in the plague-enriched areas of the country were described. The study summarised the characteristics of phenotypic and molecular genetic properties of 1220 Y. pestis strains isolated from different sites in natural plague foci of the country during the period 2010-2023. As a result, 94.8% of Y. pestis strains were typical of these plague foci, and 5.2% of strains had altered properties in some respects. To obtain information on genetic diversity and their geographical distribution, 82 DNA samples of Y. pestis strains were studied. Three phylogenetic trees were constructed, GIS maps were compiled and a gene bank, a biorepository of molecular characteristics was created to obtain specific genetic characteristics of strains and a complete picture of the genetic parameters of the plague pathogen isolated from various sites in natural foci of Kazakhstan.