Pdif-mediated antibiotic resistance genes transfer in bacteria identified by pdifFinder.

The article focuses on the development and application of pdifFinder, a web server based on the PdifSM algorithm, designed to identify plasmid dif (pdif) site-associated antibiotic resistance gene (ARG) modules in bacterial genomes. Analysis of nearly 32,000 plasmids from 717 bacterial species revealed 481 plasmids across 25 genera containing pdif-ARG modules, indicating that the XerCD-dif site-specific recombination system may facilitate horizontal transfer of ARGs both within and between genera. The study highlights the diversity of ARGs embedded in pdif modules, their variable gene content, and genus-specific base preferences in pdif sites, suggesting an evolutionary adaptation of this recombination mechanism. The identification of pdif-ARG modules provides new insights into multidrug resistance (MDR) dissemination and offers a tool for further research aimed at controlling the spread of MDR bacteria in clinical settings.