Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria

Abstract

Introduction: Type IV secretion systems (T4SSs) are integral parts of the conjugation process in enteric bacteria. These secretion systems are encoded within the transfer (tra) regions of plasmids, including those that harbor antimicrobial resistance (AMR) genes. The conjugal transfer of resistance plasmids can lead to the dissemination of AMR among bacterial populations.Methods: To facilitate the analyses of the conjugation-associated genes, transfer related genes associated with key groups of AMR plasmids were identified, extracted from GenBank and used to generate a plasmid transfer gene dataset that is part of the Virulence and Plasmid Transfer Factor Database at FDA, serving as the foundation for computational tools for the comparison of the conjugal transfer genes. To assess the genetic feature of the transfer gene database, genes/proteins of the same name (e.g., traI/TraI) or predicted function (VirD4 ATPase homologs) were compared across the different plasmid types to assess sequence diversity. Two analyses tools, the Plasmid Transfer Factor Profile Assessment and Plasmid Transfer Factor Comparison tools, were developed to evaluate the transfer genes located on plasmids and to facilitate the comparison of plasmids from multiple sequence files. To assess the database and associated tools, plasmid, and whole genome sequencing (WGS) data were extracted from GenBank and previous WGS experiments in our lab and assessed using the analysis tools.Results: Overall, the plasmid transfer database and associated tools proved to be very useful for evaluating the different plasmid types, their association with T4SSs, and increased our understanding how conjugative plasmids contribute to the dissemination of AMR genes.

Genotypic analyses of IncHI2 plasmids from enteric bacteria

“…To predict which putative plasmid transfer genes are present in the IncHI2 plasmids, the FASTA-formatted plasmid sequence files were submitted to the FDA Virulence and Plasmid Transfer Factor (VPTF) Database and searched with the Plasmid Transfer Factor Profile Comparison tool ( https://virulence.fda.gov/tools/virulenceassess) 42 . The VPTF database contains sequences for type 4 secretion system genes for multiple incompatibility groups of resistance plasmids associated with enteric bacteria.…”

Genetic relatedness and virulence potential of Salmonella Schwarzengrund strains with or without an IncFIB-IncFIC(FII) fusion plasmid isolated from food and clinical sources

“…9.0, Qiagen, Redwood City, CA, United States). FASTA files of sequence assemblies from each strain were analyzed using the multiple sequence Comparison tool within the FDA Virulence and AMR Plasmid Transfer Factor Database, 1 which targets 594 putative Salmonella virulence genes and plasmid transfer genes from key AMR plasmid Inc. groups (Aljahdali et al, 2020;Tate et al, 2022;Algarni et al, 2023). The predicted presence and absence data for the putative virulence and plasmid transfer genes were downloaded from the database, transformed to binary data and imported into BioNumerics for phylogenetic analyses of the virulence and plasmid transfer genes.…”