Genomic Characterisation of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates from a Tertiary-Care Hospital in Türkiye

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global health threat driven by limited treatment options and high-risk clones. This study aimed to characterise the clonal structure, resistance and virulence determinants and carbapenemase-carrying genetic elements of CRKP isolates from a tertiary-care hospital in Türkiye. Twenty-five isolates, one per patient, were collected between October 2023 and October 2024, tested against EUCAST criteria and sequenced with Oxford Nanopore long reads. Analyses comprised MLST, 2335-locus cgMLST, resistome, virulome, plasmid (MOB-suite), pan-genome (Panaroo) and defence-system profiling. All isolates were carbapenem-resistant, 19 ceftazidime-avibactam-resistant and seven colistin-resistant. Six sequence types and five genetic clusters were identified, with ST147 predominant (n = 13). The commonest carbapenemase profile was blaNDM-5 plus blaOXA-48 (n = 13), followed by blaKPC-3 alone (n = 5) and blaNDM-7 alone (n = 2). blaNDM-5 and blaOXA-48 were mainly carried by conjugative plasmids pAA405 and pAA002, whereas four isolates carried carbapenemases on chromosome-associated or IncX3 elements. blaNDM-5 co-occurred with the aerobactin operon in 15 isolates. The pan-genome comprised 7377 gene clusters, and isolates within a genetic cluster differed phenotypically and genotypically. Resistance and virulence determinants converged within ST147 and on shared plasmids, so genomic surveillance should consider genetic cluster, element architecture and accessory genome together.