Comparative genome analysis of carbapenemase-producing Pseudomonas aeruginosa: gene diversity, clonal distribution,...

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) represents a major health threat due to its extensive resistance to last‑resort antibiotics. Although carbapenemase determinants are key drivers of global CRPA dissemination, comprehensive genomic investigations delineating their chromosomal versus plasmid contexts are sparse. Therefore, in this study we conducted an integrated comparative genomic analysis of P. aeruginosa strains harboring major carbapenemase genes (bla_GES, bla_KPC, bla_SPM, bla_NDM, bla_VIM, and bla_IMP), with a focus on their genomic localization, surrounding genetic architectures, and associated mobility elements. Chromosomes and plasmids carrying carbapenemase genes (retrieved from GenBank through 2025) were systematically characterized for sequence types, genetic environments, co‑occurring antimicrobial resistance genes (ARGs), and plasmid mobility features using established bioinformatic pipelines. Genetic relatedness of plasmids was inferred via ClustAGE and UPGMA clustering. Multilocus sequence typing (MLST) was employed to assess clonal relatedness of isolates. Among 398 carbapenemase-carrying genomic fragments, bla_VIM, bla_KPC, and bla_GES were the most prevalent. bla_VIM, bla_IMP, and bla_NDM showed broad geographic distribution. High-risk clones including ST235, ST111, ST233, ST357, ST308, and ST277 were among the most common sequence types. Notably, a minority (10.28%) of carbapenemase-carrying plasmids were predicted to be conjugative or mobilizable. The mex, and opr families, and sul1 were most frequent co-existing ARGs. These findings highlight the dominant role of established high-risk lineages and integrative mobile elements in shaping the epidemiology of resistance. The relatively low frequency of self-transmissible plasmids suggests that horizontal resistance dissemination is likely mediated through a combination of integrative mobile genetic elements and clonal expansion. Our results underscore the necessity for enhanced genomic surveillance strategies that integrate clonal tracking with mobile resistance determinant monitoring to better understand and control the spread of carbapenem resistance.