Lineage-specific evolution and resistance-virulence divergence in Klebsiella pneumoniae ST268: a global population genomic analysis.

Abstract

Klebsiella pneumoniae sequence type 268 (ST268) represents an emerging high-risk clone with significant clinical implications. Here, we present a comprehensive genomic analysis of 562 ST268 isolates collected from 44 countries across six continents between 2001 and 2024. Phylogenomic reconstruction revealed 10 distinct lineages with diverse geographic and functional signatures. Bayesian analysis dated the emergence of ST268 to ~1,908 (95% confidence interval [CI]: 1,841-1,952), with Europe as the likely origin. Our findings uncovered a clear evolutionary split between hypervirulent and multidrug-resistant subclones. Lineages L1 and L3 were enriched for carbapenemase genes (66.1% and 60%) and acquired genes involved in inorganic ion transport and amino acid metabolism, while L2 and L6 showed preferential carriage of hypervirulence markers and gene acquisitions related to secretion systems. Plasmid profiling revealed distinct virulence and resistance plasmid populations, with notable co-occurrence in 48 isolates predominantly from lineages L2 and L6, yet minimal integration between these elements. Nonsynonymous single-nucleotide polymorphisms further revealed lineage-specific functional variations, potentially driven by distinct ecological pressures. Phenotypic validation in Galleria mellonella and mouse models confirmed the high virulence of L2 and L6 strains. These patterns suggest a functional trade-off between resistance and virulence among ST268 lineages, likely shaped by parallel evolution under selective constraints. Our study provides novel insights into the genomic architecture and adaptive divergence of ST268, highlighting the need for lineage-informed surveillance and intervention strategies to mitigate its ongoing global dissemination.