pdifFinder

pdifFinder identifies modules of antibiotic resistance genes (ARGs) flanked by inverted-repeat Xer-specific recombination sites (pdif sites) in bacterial plasmid sequences to characterize pdif-mediated horizontal gene transfer.

Key Features:

• PdifSM algorithm: Implements the PdifSM algorithm to predict diverse pdif-ARG modules across plasmids and bacterial species.
• Large-scale plasmid analysis: Analyzed nearly 32,000 plasmids from 717 bacterial species and identified 481 plasmids containing pdif sites associated with ARGs.
• pdif sequence characterization: Identifies 28-bp pdif sequences with genus-specific base preferences across different genera.
• Evolutionary and functional inference: Uses multiple sequence alignment and evolutionary analyses to reveal adaptation of the XerCD-dif site-specific recombination mechanism facilitating pdif-mediated ARG transfer.
• Mutation and module composition analysis: Detects mutations in pdif sites and diverse module architectures containing variable numbers of ARGs, insertion sequences, and other functional genes.

Scientific Applications:

• Study of horizontal gene transfer: Enables identification and characterization of pdif-mediated ARG modules to investigate mechanisms of horizontal gene transfer in bacteria.
• Evolutionary analysis of recombination systems: Supports investigation of XerCD-dif recombination adaptation and its role in interspecies and intergenera ARG transfer.
• Characterization of multidrug-resistance modules: Facilitates analysis of module composition (ARGs, insertion sequences, other genes) relevant to the spread and surveillance of multidrug-resistant bacteria and clinical mitigation strategies.

Methodology:

Developed the PdifSM prediction algorithm; analyzed a large plasmid dataset (nearly 32,000 plasmids from 717 bacterial species); and performed multiple sequence alignment, evolutionary analyses, and mutation analyses to detect and characterize pdif sites and pdif-ARG module architectures.