{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T11:59:10Z","timestamp":1776513550432,"version":"3.51.2"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,10,5]],"date-time":"2023-10-05T00:00:00Z","timestamp":1696464000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Research Foundation of South Africa","award":["120192"],"award-info":[{"award-number":["120192"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Plasmids 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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We 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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The code developed in this work is available at https:\/\/github.com\/AbeelLab\/plasmidHGT.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad612","type":"journal-article","created":{"date-parts":[[2023,10,5]],"date-time":"2023-10-05T17:32:26Z","timestamp":1696527146000},"source":"Crossref","is-referenced-by-count":14,"title":["SHIP: identifying antimicrobial resistance gene transfer between plasmids"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7219-0478","authenticated-orcid":false,"given":"Marco","family":"Teixeira","sequence":"first","affiliation":[{"name":"Faculty of Engineering, University of Porto , Porto 4200-465, Portugal"},{"name":"INESC TEC\u2014Institute for Systems and Computer Engineering, Technology and Science , Porto 4200-465, Portugal"},{"name":"Delft Bioinformatics Lab, Delft University of Technology , Van Mourik Broekmanweg 6 , Delft 2628 XE, The Netherlands"}]},{"given":"Stephanie","family":"Pillay","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology , Van Mourik Broekmanweg 6 , Delft 2628 XE, The Netherlands"}]},{"given":"Aysun","family":"Urhan","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics Lab, Delft University of Technology , Van Mourik Broekmanweg 6 , Delft 2628 XE, The Netherlands"},{"name":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard , Cambridge, MA 02142, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7205-7431","authenticated-orcid":false,"given":"Thomas","family":"Abeel","sequence":"additional","affiliation":[{"name":"Delft Bioinformatics 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