The genomic landscape of Klebsiella pneumoniae in Russia

Klebsiella pneumoniae is a critical priority pathogen known for its extensive antimicrobial resistance (AMR) and capacity to cause severe infections. The traditional dichotomy between multidrug-resistant (MDR) and hypervirulent strains is rapidly eroding, driving the emergence of highly lethal convergent phenotypes. While global surveillance heavily emphasizes KPC-producing lineages, the specific genomic architecture driving this convergence in the Russian Federation remains insufficiently resolved. In this study, we analyzed population structure represented in a curated dataset 264 K. pneumoniae genomes, comprising 18 newly sequenced clinical isolates and 246 public assemblies from 2015 to 2024, using whole-genome sequencing, pangenome reconstruction, resistome, virulence factors and plasmidome profiling, and CRISPR-Cas typing. Our analysis revealed that high-risk sequence types ST395 (56.1%) and ST147 (8.7%) dominate the regional landscape. Carbapenemase genes were detected in 76.5% of isolates, primarily driven by bla_OXA−48 on IncL/M plasmids within ST395 and bla_NDM variants in ST147. Crucially, 46.2% of isolates harbored convergent plasmids, predominantly large, mosaic IncFIB/IncHI1B cointegrates, that simultaneously encode hypervirulence determinants like the aerobactin synthesis locus alongside resistance genes including bla_NDM−1 and bla_CTX−M−15. Additionally, we identified a heavy enrichment of plasmid-borne Type IV-A3 CRISPR-Cas systems in the dominant ST395 clone. The regional dominance of ST395 and ST147, coupled with the extensive horizontal integration of both resistance and virulence, represents a formidable public health threat. These findings underscore the critical need for localized genomic surveillance to effectively monitor evolving convergent pathogens and guide tailored antimicrobial stewardship.