Integrated Phenotypic, Molecular, and Genomic Analysis of Antimicrobial Resistance in Yersinia pestis Isolates from Natural Plague Foci of Kazakhstan

Plague remains a globally important zoonotic disease maintained in natural foci, with ongoing epizootic activity and periodic human cases reported in several regions of the world. Continuous monitoring of antimicrobial susceptibility in Yersinia pestis is essential because the emergence of resistant strains could compromise the effectiveness of currently recommended therapeutic regimens. In this study, 75 Y. pestis isolates originating from natural plague foci of Kazakhstan were investigated using an integrated approach combining phenotypic susceptibility testing, targeted molecular screening, and whole-genome sequencing (WGS)-based resistome analysis. The collection included historical clinical isolates obtained during plague outbreaks as well as more recent epizootic strains recovered from animal hosts and flea vectors. Phenotypic testing demonstrated uniformly high susceptibility to clinically relevant antimicrobial agents used for plague treatment. Targeted molecular screening by real-time PCR did not detect the analyzed resistance determinants. Genome-wide analysis based on WGS data from NCBI BioProject PRJNA1249055 did not identify acquired antimicrobial resistance genes, major resistance-associated mutations in key chromosomal loci (rpsL, gyrA, and parC), or plasmid-borne resistance determinants. Regulatory loci associated with adaptive responses were highly conserved across the analyzed genomes. The complete concordance between phenotypic, molecular, and genomic findings indicates a stable antimicrobial susceptibility profile of Y. pestis circulating in natural plague foci of Kazakhstan. These results support the continued effectiveness of current therapeutic strategies for plague and highlight the value of integrating genomic surveillance into long-term monitoring programs for this pathogen.