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For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a <jats:italic>bla<\/jats:italic>\n                  <jats:sub>CTX-M-15<\/jats:sub> gene conferring extended-spectrum beta-lactamase (ESBL) resistance in <jats:italic>Salmonella enterica<\/jats:italic> serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in <jats:italic>Enterobacterales<\/jats:italic>, in this study we carried out a follow-up retrospective analysis of UK <jats:italic>Salmonella<\/jats:italic> isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47\u200a784 isolates for the presence of the P1 lytic replication gene <jats:italic>repL<\/jats:italic>, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170\/226) belonged to <jats:italic>S<\/jats:italic>. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2\u2009kb in size, with an average length of 92.1\u2009kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in <jats:italic>Salmonella<\/jats:italic>, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.<\/jats:p>","DOI":"10.1099\/mgen.0.001247","type":"journal-article","created":{"date-parts":[[2024,5,8]],"date-time":"2024-05-08T15:18:12Z","timestamp":1715181492000},"source":"Crossref","is-referenced-by-count":4,"title":["Presence of phage-plasmids in multiple serovars of Salmonella enterica"],"prefix":"10.1099","volume":"10","author":[{"given":"Satheesh","family":"Nair","sequence":"first","affiliation":[{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clare R.","family":"Barker","sequence":"additional","affiliation":[{"name":"NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK"},{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Bird","sequence":"additional","affiliation":[{"name":"NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK"},{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David R.","family":"Greig","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK"},{"name":"NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK"},{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caitlin","family":"Collins","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge, Cambridge, UK"},{"name":"NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK"},{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana\u00efs","family":"Painset","sequence":"additional","affiliation":[{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie","family":"Chattaway","sequence":"additional","affiliation":[{"name":"NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK"},{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Derek","family":"Pickard","sequence":"additional","affiliation":[{"name":"The Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lesley","family":"Larkin","sequence":"additional","affiliation":[{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saheer","family":"Gharbia","sequence":"additional","affiliation":[{"name":"NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK"},{"name":"NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK"},{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xavier","family":"Didelot","sequence":"additional","affiliation":[{"name":"School of Public Health and Department of Statistics, University of Warwick, Warwick, UK"},{"name":"NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK"},{"name":"NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5599-3933","authenticated-orcid":false,"given":"Paolo","family":"Ribeca","sequence":"additional","affiliation":[{"name":"NIHR Health Protection Research Unit in Genomics and Enabling Data, University of Warwick, Warwick, UK"},{"name":"NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK"},{"name":"Biomathematics and Statistics Scotland, The James Hutton Institute, Edinburgh, UK"},{"name":"UK Health Security Agency, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"345","reference":[{"key":"R1","article-title":"World Health Organization. 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