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In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.

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Two new web tools, PlasmidFinder and pMLST, aid in identifying and characterizing plasmids from whole-genome sequencing data of Enterobacteriaceae. These tools facilitate bacterial typing and detection of antimicrobial resistance-associated plasmids.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Enterobacteriaceae are clinically relevant pathogens often carrying antimicrobial resistance genes on plasmids.
  • Accurate detection and characterization of plasmids are crucial for bacterial typing and understanding antimicrobial resistance.
  • Existing methods for plasmid analysis can be time-consuming and complex.

Purpose of the Study:

  • To design and develop user-friendly web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data.
  • To facilitate rapid identification of known plasmid types within multidrug-resistant Enterobacteriaceae species.
  • To aid in bacterial typing using draft genomes and plasmid sequencing data.

Main Methods:

  • Collected 559 fully sequenced Enterobacteriaceae plasmids from NCBI to build a consensus database for PlasmidFinder.
  • Integrated a weekly updated database from pubmlst.org into the pMLST web tool for plasmid multilocus sequence typing.
  • Evaluated both web tools using draft genomes from Salmonella enterica serovar Typhimurium isolates.

Main Results:

  • PlasmidFinder identified 103 replicons and 0-5 different plasmid replicons per genome in 49 S. Typhimurium draft genomes.
  • The pMLST web tool successfully subtyped plasmid genomic sequencing data, identifying known and novel alleles and sequence types (STs).
  • Both tools demonstrated broad detection capabilities for plasmids associated with antimicrobial resistance.

Conclusions:

  • The developed web tools (PlasmidFinder and pMLST) are effective for analyzing plasmid sequences from WGS data.
  • These tools can rapidly detect and characterize plasmids, aiding in the study of antimicrobial resistance in Enterobacteriaceae.
  • The tools facilitate bacterial typing and provide valuable insights into plasmid diversity and evolution.