Whole-genome sequencing reveals the genomic characterization and evolution of carbapenem-resistant Klebsiella pneumoniae in Gansu, China

Introduction Klebsiella pneumoniae has emerged as a major opportunistic pathogen, with rising antimicrobial resistance representing a critical public health concern. This study investigated the genomic characteristics, transmission dynamics, and evolutionary relationships of CRKP isolates from Gansu Province, China, to inform regional prevention strategies. Methods Thirty CRKP isolates collected from two tertiary hospitals (2023-2025) were tested for susceptibility to 15 antibiotics and subjected to whole-genome sequencing. Genome assembly and annotation employed standard pipelines, followed by multilocus sequence typing, capsular typing, phylogenetic reconstruction, pan-genome, and mobile genetic element analyses. Comparative genomic and statistical analyses were performed with publicly available data. Results Most isolates originated from sputum (40%) and blood (23.3%) and were resistant to over 90% of β-lactam and carbapenem agents. Their genomes (5.2-5.8 Mb) contained on average 5,596 coding sequences. ST11 predominated (88.46%), mainly associated with KL25 (64.29%) and KL64 (17.86%) capsule types. The plasmid-borne blaKPC-2 gene occurred in 79.31% of isolates, while virulence factors (rmpA, rmpA2, iuc) were enriched in ST11-KL25/KL64 lineages (p<0.05). Phylogenomic analysis showed limited genetic diversity (median SNP = 103.5), consistent with clonal spread and potential hospital transmission. Pan-genome comparisons revealed that ST11-KL25 and ST11-KL64 strains shared a conserved core genome but overlapped with non-ST11 strains by only 6.28%, highlighting substantial genomic flexibility across capsule types. Conclusions The ST11-KL25 CRKP lineage shows enhanced adaptation and may become or is becoming the dominant clone in Gansu. These results highlight the necessity for continuous, longitudinal genomic surveillance to curb the spread of highly resistant K. pneumoniae .