Molecular epidemiology of carbapenemase-carrying Klebsiella pneumoniae in China: Distribution of carbapenemase types, capsular serotypes, and virulence factors.

We conducted a large-scale genomic analysis of 9,082 carbapenemase-producing Klebsiella pneumoniae (CPKP) isolates originating from China and collected between 2005 and 2024, using genomes retrieved from the NCBI database. The aim was to characterize population structure, resistance determinants, capsular diversity, and virulence-associated loci at a national scale. The CPKP population exhibited substantial genetic diversity, encompassing 233 sequence types (STs), 109 capsular serotypes (KLs), and a wide range of carbapenemase genes. KPC-2-producing ST11 was the dominant epidemic lineage nationwide and remained prevalent throughout the study period. Within ST11, a temporal shift in capsular serotypes was observed, with KL47 predominating during 2013–2015 and KL64 becoming dominant from 2016 onward, while both serotypes persisted at substantial frequencies. In contrast, metallo-β-lactamases such as NDM-1, NDM-5, and IMP-4 showed heterogeneous clonal distributions without a single dominant lineage. Carbapenem-producing isolates belonging to hypervirulence-associated capsular serotypes (KL1 and KL2) were detected sporadically. KL1-type CPKP isolates were predominantly associated with ST23 and carried multiple classical virulence-associated loci, whereas KL2-type CPKP isolates were distributed across diverse STs and exhibited more variable virulence gene carriage. Carbapenemase-producing KL1 and KL2 isolates were first detected in this dataset in 2013 in different regions of China. Virulence gene distribution was strongly structured by capsular serotype and clonal background. Classical hypervirulence-associated loci, including aerobactin, salmochelin, colibactin, and regulators of the mucoid phenotype (rmpADC), were largely confined to KL1 and a subset of KL2 lineages and were infrequently detected among the major carbapenem-producing clones, ST11 and ST15. In contrast, yersiniabactin was widespread among CPKP isolates but showed lineage-specific associations with distinct ICEKp elements. Resistance-associated plasmid backbones, including ColRNAI, IncFIB/IncHI1B, and IncFII, were commonly detected. Overall, this study provides a comprehensive population-level overview of CPKP in China and highlights the expansion of highly resistant clones alongside a limited and structured distribution of classical hypervirulence determinants.