Emergence and genomic characterization of hypervirulent ST23/K1 Klebsiella pneumoniae: local epidemiology and global context

TL;DR

This study analyzes the genomic diversity and virulence of K1/ST23 Klebsiella pneumoniae in the Czech Republic, revealing high virulence and evolving resistance through plasmid exchange.

Contribution

The study provides new insights into the genomic evolution and virulence mechanisms of K1/ST23 Klebsiella pneumoniae in a European context.

Findings

The Czech K1/ST23 KP population is highly virulent but genomically diverse, with multiple phylogenetic lineages.

Virulence genes are frequently integrated into plasmids or chromosomes via insertion sequences, promoting resistance evolution.

Emerging fusion plasmids suggest a path toward multidrug-resistant hypervirulent K. pneumoniae.

Abstract

Hypervirulent Klebsiella pneumoniae (hvKp) of the K1/ST23 lineage is an emerging global threat associated with invasive community-acquired infections. Increasing reports of virulence–resistance convergence highlight the need for genomic surveillance, particularly within Europe where data remain limited. This study characterizes clinical K1/ST23 KP isolates circulating in the Czech Republic and compares them to a global genomic background to evaluate virulence architecture, resistance acquisition and plasmid evolution.

From 2017 to 2025, 570 K. pneumoniae isolates from a tertiary-care hospital were screened for hvKp markers. Ninety-six K1/ST23 isolates were subjected to long-read whole-genome sequencing and plasmid reconstruction. Genomes were analyzed alongside 2,463 international ST23 datasets using core-SNV phylogenomics, virulence/resistance profiling, and structural plasmid mapping. Chromosomal integrations were examined through analysis of flanking insertion-sequence contexts.

The Czech K1/ST23 KP population exhibited high virulence uniformity (95/96 isolates scoring 9/9) without evidence of a single-clone outbreak, instead forming multiple phylogenetic lineages consistent with recurrent introductions. Eighty-three isolates carried pLVPK-like virulence plasmids; however, structural plasticity was prominent. The iro cluster was relocated to conjugative IncFII/rep_cluster_1418 plasmids in two isolates—one carrying additional AMR genes—and was chromosomally integrated via IS1-mediated recombination in three others. Iut was chromosomally integrated via IS903 (IS5 family) with either classical target-site duplication or recombination-associated insertion. Nine virulence–resistance fusion plasmids (IncFIB–IncFII–IncHI1B or IncC-based) were identified, representing early convergence toward MDR-hvKp.

K1/ST23 KP circulating in the Czech Republic is highly virulent yet genomically diverse, driven by active plasmid exchange, insertion-sequence–mediated chromosomal integration, and emerging virulence–resistance fusion plasmids. Although carbapenemase genes were absent, ESBL determinants and transmissible virulence loci indicate strong evolutionary potential toward MDR-hvKp. Continuous genomic surveillance and early intervention strategies are essential to mitigate future clinical impact.

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