ArticleBioinformatics (Oxford, England)2023
SHIP: identifying antimicrobial resistance gene transfer between plasmids.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 13 citations in OpenAlex.
- pLAST-a tool for rapid comparison and classification of bacterial plasmid sequences.Bioinformatics (Oxford, England) · 2026Article
- Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.Antimicrobial agents and chemotherapy · 2025Review
- Isolation and Characterization of Colistin-ResistantMicroorganisms · 2025Article
- Antimicrobial Resistance Profile of Zoonotic Clinically Relevant WHO Priority Pathogens.Pathogens (Basel, Switzerland) · 2024Article
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationPlasmids are carriers for antimicrobial resistance (AMR) genes and can exchange genetic material with other structures, contributing to the spread of AMR. There is no reliable approach to identify the transfer of AMR genes across plasmids. This is mainly due to the absence of a method to assess the phylogenetic distance of plasmids, as they show large DNA sequence variability. Identifying and quantifying such transfer can provide novel insight into the role of small mobile elements and resistant plasmid regions in the spread of AMR.
resultsWe developed SHIP, a novel method to quantify plasmid similarity based on the dynamics of plasmid evolution. This allowed us to find conserved fragments containing AMR genes in structurally different and phylogenetically distant plasmids, which is evidence for lateral transfer. Our results show that regions carrying AMR genes are highly mobilizable between plasmids through transposons, integrons, and recombination events, and contribute to the spread of AMR. Identified transferred fragments include a multi-resistant complex class 1 integron in Escherichia coli and Klebsiella pneumoniae, and a region encoding tetracycline resistance transferred through recombination in Enterococcus faecalis. AVAILABILITY AND IMPLEMENTATION: The code developed in this work is available at https://github.com/AbeelLab/plasmidHGT.
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