Genomic epidemiology reveals niche specialization and a virulence-resistance trade-off in ST23 and ST11 hypervirulent Klebsiella pneumoniae.

Abstract

Objectives: The convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae poses a critical public health threat, yet the comparative genomic characteristics and adaptation patterns of dominant clones ST23 and ST11 in clinical settings remain unclear. This study aimed to characterize their divergent adaptive strategies.

Methods: We performed whole-genome sequencing on 824 hvKP isolates derived from 2,193 clinical Klebsiella pneumoniae isolates collected at a National Regional Medical Center in Central China. Among these, ST23 (n=199) and ST11 (n=140) represented the two predominant sequence types and were compared regarding antimicrobial resistance profiles, resistance determinants, virulence determinants, plasmid replicon types, and phylogenetic relationships using comparative genomic, phylogenetic, and co-acquisition analyses.

Results: ST23-hvKP was primarily associated with surgical and medical departments, largely antibiotic-susceptible (MDR 33.7%, CR 1.0%), with near-complete virulence gene profiles (iuc 99.5%, iro 97.5%). Conversely, ST11-hvKP was predominantly ICU-associated and extensively drug-resistant (MDR 97.9%, CR 93.6%), characterized by frequent bla_KPC-2 carriage (95.7%) and a highly prevalent IncFII(pHN7A8) replicon (98.6%), with bla_KPC-2 strongly associated with IncFII(pHN7A8), but with an incomplete virulence profile (iro 0.7%). Resistance-hypervirulence convergence was markedly higher in ST11 (92.1%) than ST23 (9.5%). Plasmid ecology and co-acquisition analysis revealed a negative correlation between resistance-associated (IncFII/IncR) and virulence-associated (IncFIB(K)) replicons, suggesting that convergence in ST11 involves coexisting distinct plasmid systems rather than detectable plasmid fusion events. Phylogenetic analysis demonstrated distinct clustering patterns between ST23 and ST11.

Conclusions: ST23 retains a classic hypervirulent phenotype, whereas ST11 represents a hospital-adapted convergent clone characterized by a complex resistome, an incomplete canonical virulence repertoire, and separate plasmid systems. This niche-specialized resistance-virulence trade-off underscores the need for clone-tailored surveillance and management strategies.