Integrative genomic and clinical analysis of carbapenem-resistant and susceptible Klebsiella pneumoniae isolates from a tertiary hospital in Wuhan

Abstract

Objectives Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a major global health threat due to its resistance to carbapenems. As the mechanisms underlying carbapenem resistance in CRKP remain incompletely understood, we seek to provide important insights into the clinical and genomic characteristics of CRKP. Methods A total of 40 CRKP and 42 carbapenem-susceptible Klebsiella pneumoniae (CSKP) isolates were collected from a tertiary hospital in Wuhan, China. Integrating 2,460 publicly available Klebsiella pneumoniae genomes, we conducted a comprehensive analysis of clinical risk factors, resistance and virulence gene profiles, plasmid replicon composition, core genome SNP-based phylogeny, pan-genome structure, and genome-wide single-nucleotide variants and insertions/deletions (SNVs/InDels) variation. Results Clinical analysis identified a Charlson comorbidity index > 3 and respiratory tract infections as independent risk factors for CRKP infection. Genomic comparisons revealed that CRKP strains harbored more resistance and virulence genes than CSKP strains, with ST11 being the dominant CRKP clone that frequently carried the blaKPC-2 gene. Phylogenetic analysis incorporating public genomes revealed regional differences in sequence type and carbapenemase genotype distributions. Pan-genome analysis demonstrated open pan-genome characteristics in both groups, with cloud genes representing the largest gene category. Comparative genomic analyses revealed distinct SNV and InDel distribution patterns between CRKP and CSKP isolates, while GO annotation of the prioritized variant-associated genes showed broad functional representation across cellular and metabolic processes, transport and responses to stimuli, membrane-associated components, and binding and catalytic functions. Conclusions CCI >3 and respiratory tract infection were independently associated with CRKP infection. ST11-blaKPC-2 was the predominant epidemic lineage and CRKP isolates carried a greater burden of resistance and virulence determinants than CSKP isolates. Phylogenetic, pan-genomic, and comparative genomic analyses revealed substantial genomic diversity and distinct genomic variation patterns between CRKP and CSKP. These findings provide insights into the clinical risk profile, clonal dynamics, and genomic evolution of CRKP, informing future surveillance and infection control strategies.