Tracing the possible evolutionary trends of : insights from molecular epidemiology and phylogenetic analysis.

, encompassing two subspecies, and , is a common opportunistic pathogen, notable for intrinsic resistance to multiple antimicrobial agents. Despite its clinical significance, research into the potential evolutionary dynamics of remains limited. This study involved the analysis of genome sequences from 431 . isolates, comprising 206 isolates that cause host infections, obtained from this study and 225 from the NCBI genome data sets. A diverse array of antimicrobial resistance genes (ARGs) was identified in isolates, including , (X4), , and various carbapenemase genes. In addition, a novel -bearing plasmid with demonstrated conjugative capability was discovered in . The majority of virulence-related genes (VRGs), except for the gene cluster, were found in almost all . Three novel genospecies of were identified, designated as , , and . Compared to , genospecies possessed a greater number of flagellar-related genes, typically located within mobile genetic elements (MGEs), suggesting potential for better environmental adaptability. Phylogenetic analysis further disclosed that was divided into 12 sequence clusters (SCs). Particularly, SC9 harbored an elevated abundance of ARGs and VRGs, mainly toxin-related genes, and was associated with a higher presence of MGEs compared to non-SC9 strains. The collective findings suggest that undergoes evolution driven by the influence of MGEs, thereby significantly enhancing its adaptability to selective pressures of environmental changes and clinical antimicrobial agents.IMPORTANCEThe growing clinical significance of arises from its abundant virulence factors and antimicrobial resistance genes, resulting in elevated infection rates and increased clinical scrutiny. However, research on the molecular epidemiology and evolutionary trends of has been scarce. Our study established a list of virulence-related genes (VRGs) for and conducted a large-scale epidemiological investigation into these VRGs. Based on genomic classification, three novel genotypes of were identified, representing evolutionary adaptations and responses to environmental challenges. Furthermore, we discovered the emergence of a sequence cluster enriched with antimicrobial resistance genes, VRGs, and mobile genetic elements, attributed to the selective pressure of antimicrobial agents. In addition, we identified a novel conjugative plasmid harboring the gene. These findings hold significance in monitoring and comprehending the epidemiology of .