Genomic epidemiology, population structure and lineage-associated genomic variation in KPC-producing Pseudomonas aeruginosa

Abstract Objectives KPC-producing Pseudomonas aeruginosa (KPC-PA) has emerged as an important multidrug-resistant pathogen, yet its population structure and lineage-associated genomic variation remain incompletely understood. We investigated the genomic epidemiology of an international collection of KPC-PA genomes to characterize population structure, evolutionary patterns, and lineage-associated genomic features. Methods A complete genome of a clinical ST463 isolate (PA328) was generated using hybrid sequencing and analyzed together with 655 publicly available KPC-PA genomes. Comparative genomic, phylogenomic, pangenome, recombination, and Bayesian temporal analyses were performed to investigate population structure and identify genomic features associated with major lineages. Results Among 656 KPC-PA genomes, bla KPC−2 (99.5%) and ST463 (43.6%) were predominant. Population genomic analysis resolved eight major phylogenetic lineages with distinct sequence-type compositions and geographic distributions, including ST463 in China, ST282 in the United States, and ST654 in Chile. Assembly-based screening identified candidate frameshift calls in genes annotated as being involved in metabolism, iron acquisition, transport, and virulence-associated functions, providing potential targets for further investigation using read-level confirmation. Descriptive analyses revealed lineage-associated patterns of antimicrobial resistance genes (ARGs) and mobile genetic elements co-occurrence. Within ST463, an operationally defined high-recombination region (HRR) contained genes annotated as being related to secretion systems, biofilm formation, metabolism, and mobile genetic elements. Bayesian analysis estimated the time to the most recent common ancestor (tMRCA) of the sampled Chinese ST463 population at approximately 2005. Partial similarity between plasmid sequences and the HRR suggested potential evolutionary connections, although their specific relationship requires further investigation. Conclusions This study characterizes the population structure and lineage-associated genomic variation of KPC-PA within a large international genome collection. The findings provide a descriptive genomic resource for understanding KPC-PA evolution and surveillance, and highlight candidate genomic features that warrant further structure-aware analyses and experimental investigation.