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SHIP: identifying antimicrobial resistance gene transfer between plasmids

Marco Teixeira1,2,3, Stephanie Pillay3, Aysun Urhan3,4

  • 1Faculty of Engineering, University of Porto, Porto 4200-465, Portugal.

Bioinformatics (Oxford, England)
|October 5, 2023
PubMed
Abstract

Insights

Antimicrobial resistance (AMR) gene transfer between plasmids is hard to track. A new method, SHIP, identifies conserved AMR gene fragments across diverse plasmids, revealing their mobilization and spread.

Area of Science:

  • Microbiology
  • Genetics
  • Bioinformatics

Background:

  • Plasmids are key vectors for antimicrobial resistance (AMR) genes, facilitating their spread.
  • Current methods lack reliability in identifying AMR gene transfer across plasmids due to high DNA sequence variability and lack of phylogenetic assessment.
  • Understanding plasmid evolution and gene transfer is crucial for combating AMR.

Purpose of the Study:

  • To develop a novel method for quantifying plasmid similarity and identifying AMR gene transfer.
  • To investigate the role of mobile genetic elements and plasmid regions in AMR dissemination.

Main Methods:

  • Developed SHIP (Similarity of mobile genetic elements based on plasmid evolution), a novel computational method to assess plasmid similarity.
  • Analyzed plasmid DNA sequences to identify conserved fragments and evidence of lateral gene transfer.
  • Investigated the mechanisms of gene transfer, including transposons, integrons, and recombination.

Main Results:

  • Identified conserved fragments containing AMR genes in structurally different and phylogenetically distant plasmids, indicating lateral transfer.
  • Demonstrated that AMR gene regions are highly mobilizable between plasmids via mobile genetic elements and recombination.
  • Found specific examples of transferred fragments, including a complex class 1 integron and a tetracycline resistance region.

Conclusions:

  • The SHIP method provides a reliable approach to quantify plasmid similarity and detect AMR gene transfer.
  • AMR genes are actively mobilized between plasmids, contributing significantly to the spread of antimicrobial resistance.
  • This work offers novel insights into the evolutionary dynamics of plasmids and AMR dissemination.

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