{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T14:42:31Z","timestamp":1793371351587,"version":"4.5.0"},"reference-count":82,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"vor","delay-in-days":151,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wellcome Discovery Award","award":["226602\/Z\/22\/Z"],"award-info":[{"award-number":["226602\/Z\/22\/Z"]}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/X003051\/1"],"award-info":[{"award-number":["BB\/X003051\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Bacterial genomes represent dynamic ecological systems in which highly dynamic accessory genome element compositions drive evolution. Emerging evidence suggests that bacterial defence systems, which protect against phages and other genetic elements, can interact cooperatively, competitively, and antagonistically to influence horizontal gene transfer, shape phage susceptibility, and diversify genomes across environments. Recent ecological studies reveal non-random co-occurrence and avoidance patterns among defence systems, suggesting that these patterns may emerge from ecological and evolutionary interactions rather than chance. Hence, these patterns need exploring in the context of ecological niche and co-localization to identify putative functional compatibilities and elucidate how defence systems shape the accessory genome. To characterize these patterns, we analysed the distributions of defence systems and other accessory genome elements in a curated global dataset of 2940 Pseudomonas aeruginosa. Defence system content varied by ecological niche, with higher numbers in non-cystic fibrosis\u2013derived isolates (average n\u2009=\u20097.9) compared to cystic fibrosis\u2013derived isolates (average n\u2009=\u20096.5). There were also multiple associations (n\u2009=\u2009426) and dissociations (n\u2009=\u200950) among defence systems, and among other accessory genome elements, many with a plausible biological explanation. We also found that defence and anti-defence systems engage in more interactions than other accessory genome element types (e.g. antimicrobial resistance genes, plasmids), suggesting that they are a major driving force in the ecological dynamics of bacterial genomes. These patterns provide new insights into the evolutionary forces shaping bacteria and provide a valuable resource of robustly quantitated interactions, establishing a baseline for future mechanistic and ecological investigations of defence system interactions.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag130","type":"journal-article","created":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T11:45:48Z","timestamp":1780055148000},"source":"Crossref","is-referenced-by-count":3,"title":["Defence systems drive accessory genome interactions in\n                    <i>Pseudomonas aeruginosa<\/i>"],"prefix":"10.1093","volume":"6","author":[{"given":"Charlotte E","family":"Chong","sequence":"first","affiliation":[{"name":"Department of Genetics, University of Cambridge , Cambridge, CB2 3EH ,","place":["United Kingdom"]},{"name":"Multi-Defence Consortium , https:\/\/sites.exeter.ac.uk\/multidefence\/ , Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, TR10 9FE ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron","family":"Weimann","sequence":"additional","affiliation":[{"name":"The Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge , Cambridge, CB2 0BB ,","place":["United Kingdom"]},{"name":"Cambridge Centre for AI in Medicine, University of Cambridge , Cambridge, CB3 0WA ,","place":["United Kingdom"]},{"name":"Department of Veterinary Medicine, University of Cambridge , Cambridge, CB3 0ES ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksei","family":"Agapov","sequence":"additional","affiliation":[{"name":"Multi-Defence Consortium , https:\/\/sites.exeter.ac.uk\/multidefence\/ , Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, TR10 9FE ,","place":["United Kingdom"]},{"name":"Environment and Sustainability Institute, Biosciences, University of Exeter , Penryn, TR10 9FE ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne L","family":"Fothergill","sequence":"additional","affiliation":[{"name":"Multi-Defence Consortium , https:\/\/sites.exeter.ac.uk\/multidefence\/ , Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, TR10 9FE ,","place":["United Kingdom"]},{"name":"Department of Clinical Infection, Microbiology and immunology, University of Liverpool , Liverpool, CH64 7TE ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0362-820X","authenticated-orcid":false,"given":"Michael A","family":"Brockhurst","sequence":"additional","affiliation":[{"name":"Multi-Defence Consortium , https:\/\/sites.exeter.ac.uk\/multidefence\/ , Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, TR10 9FE ,","place":["United Kingdom"]},{"name":"Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester , Manchester, M13 9PL ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julian","family":"Parkhill","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge , Cambridge, CB3 0ES ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R Andres","family":"Floto","sequence":"additional","affiliation":[{"name":"The Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge , Cambridge, CB2 0BB ,","place":["United Kingdom"]},{"name":"Cambridge Centre for Lung Infection, Royal Papworth Hospital , Cambridge, CB2 0AY ,","place":["United Kingdom"]},{"name":"Department of Medicine, University of Cambridge , Cambridge, CB2 0SP ,","place":["United Kingdom"]},{"name":"Cambridge University Hospitals Trust , Cambridge, CB2 0QQ ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark D","family":"Szczelkun","sequence":"additional","affiliation":[{"name":"Multi-Defence Consortium , https:\/\/sites.exeter.ac.uk\/multidefence\/ , Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, TR10 9FE ,","place":["United Kingdom"]},{"name":"DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol , Bristol, BS8 1TD ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edze R","family":"Westra","sequence":"additional","affiliation":[{"name":"Multi-Defence Consortium , https:\/\/sites.exeter.ac.uk\/multidefence\/ , Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, TR10 9FE ,","place":["United Kingdom"]},{"name":"Environment and Sustainability Institute, Biosciences, University of Exeter , Penryn, TR10 9FE ,","place":["United 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