Molecular Tracing and Comparative Genomics Analysis of Yersinia pestis Strains Isolated from Wild Rodents in Yunnan Province in 2022

Three episodes of sylvatic plague occurred in Yunnan from April to November 2022, and nine <i>Yersinia pestis</i> strains were isolated. Whole-genome sequencing was performed on these isolates, and phylogenetic analysis based on SNP comparisons included 234 publicly available genomes from NCBI. All nine 2022 strains clustered within the 1.IN5 lineage, together with historical isolates from the Lijiang wild rodent plague focus. The Heqing strain HQ1 was most closely related to previous Heqing isolates, while seven Lijiang 2022 strains formed a monophyletic cluster with historical Lijiang strains; the remaining strain LJ4 was the closest relative to this cluster. Whole-genome comparison of HQ1 with historical Heqing strains revealed six SNPs and two indels. Of these, one nonsynonymous SNP and both indels-one being a deletion in the flagellin gene flgF-were located in coding regions. Comparison of the Lijiang strain 2022YL002 with historical local isolates identified ten SNPs and three indels. Five nonsynonymous SNPs were found in coding regions, including one at position 1566343 causing an amino acid change in the iron uptake regulator Fur, a virulence-associated mutation. All three indels were in coding regions. These findings confirm that the 2022 outbreaks originated from local plague reservoirs, while genetic differences indicate ongoing bacterial evolution. The results underscore the persistent activity of sylvatic plague in the Lijiang area and highlight the need for continued surveillance to prevent human spillover.