Emergence of carbapenem-resistant putative hypervirulent Klebsiella pneumoniae ST147 with a distinct hybrid plasmid in Türkiye

Abstract

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) represents a growing clinical threat due to convergence of resistance and virulence determinants. We conducted a multicenter genomic epidemiology study analyzing CR-hvKp isolates collected from 19 tertiary-care hospitals across Türkiye between 2018 and 2023. CR-hvKp isolates were subjected to whole-genome sequencing to investigate resistance and virulence determinants, plasmid replicon profiles, and phylogenetic relationships. The proportion of CR-hvKp among CR-Kp increased from 20.7% in 2018 to 33.1% by 2023. We identified ST2096 as the predominant clone in 2018–2019, largely associated with blaOXA-232. However, after 2022, ST147 emerged as the dominant CR-hvKp lineage, characterized by co-carriage of blaNDM-5 and blaOXA-48, KL64 capsule and exhibiting high antimicrobial resistance scores. Long-read sequencing revealed a 364-kb hybrid plasmid in an ST147 isolate, harboring IncHI1B_pNDM and IncFIB_pNDM replicons. Notably, the ST147 hybrid plasmid (pPF302_hybrid) carried rmtF1 and arr-2, resistance genes that have not been previously reported in hybrid plasmids linked to ST147. These findings indicate ongoing acquisition of resistance determinants in ST147 and highlight its increased adaptive potential under antimicrobial pressure. Our results demonstrate a clear clonal shift in Türkiye’s CR-hvKp population from ST2096 to ST147, alongside evolving resistance patterns and the emergence of hybrid plasmids. These insights emphasize the need for ongoing genomic surveillance and robust molecular characterization in regions facing high CR-hvKp prevalence.