{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:49:34Z","timestamp":1787010574265,"version":"build-2736575974"},"reference-count":60,"publisher":"Microbiology Society","issue":"3","license":[{"start":{"date-parts":[[2025,3,28]],"date-time":"2025-03-28T00:00:00Z","timestamp":1743120000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008398","name":"Villum Fonden","doi-asserted-by":"crossref","award":["35946"],"award-info":[{"award-number":["35946"]}],"id":[{"id":"10.13039\/100008398","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,28]]},"abstract":"<jats:p>\n                    RP4, RP1, RK2 and R68 were isolated from the multidrug-resistant bacterial wound isolates in 1969 in the Birmingham Accident Hospital, Birmingham, England, and collectively called Birmingham-group IncP-1\n                    <jats:italic>\u03b1<\/jats:italic>\n                    plasmids. These plasmids have been widely used as models to study different aspects of plasmid biology, develop genetic delivery systems and design plasmid vectors. Early studies showed that these plasmids conferred the same antibiotic resistance profile, had a similar size and were undistinguishable from each other using DNA heteroduplex electron microscopy and restriction endonuclease analyses. These observations have led to the widely held assumption that they are identical, although there has been no conclusive supporting evidence. In this work, we sequenced the plasmids RP1 and RP4 from our laboratory strain collection and compared these new sequences with the plasmids RP4 and RK2 assembled from a publicly available sequencing database, showing that the RP1, RP4 and RK2 plasmids are 60\u2009095 bp in length and identical at the nucleotide resolution. Noteworthily, the plasmid sequence is highly conserved despite having been distributed to different labs over 50\u2009years and propagated in different bacterial hosts, strengthening the previous observation that the bacterial host adapts to the RP4\/RP1\/RK2 plasmid rather than the opposite. In the updated RP4\/RP1\/RK2 sequence, we found a fusion gene, called\n                    <jats:italic>pecM-orf2<\/jats:italic>\n                    , that was formed putatively by a genetic deletion event. By searching for\n                    <jats:italic>pecM-orf2<\/jats:italic>\n                    in the National Center for Biotechnology Information database, we detected remnants of the RP4\/RP1\/RK2 plasmid that carry features of laboratory-engineered vectors in bacterial environmental isolates, either in their chromosome or as a plasmid. This suggests a leak of these plasmids from the laboratory into the environment, which may subsequently impact bacterial evolution and raises concerns about the biocontainment of engineered plasmids when being handled in laboratory settings.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001381","type":"journal-article","created":{"date-parts":[[2025,3,28]],"date-time":"2025-03-28T12:37:36Z","timestamp":1743165456000},"source":"Crossref","is-referenced-by-count":2,"title":["Birmingham-group IncP-1\u03b1 plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates"],"prefix":"10.1099","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9576-5246","authenticated-orcid":false,"given":"Vuong Van Hung","family":"Le","sequence":"first","affiliation":[{"name":"Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark"},{"name":"Faculty of Health and Life Sciences, University of Exeter, Exeter, UK"},{"name":"Living Systems Institute, University of Exeter, Exeter, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuang","family":"Gong","sequence":"additional","affiliation":[{"name":"Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorrie","family":"Maccario","sequence":"additional","affiliation":[{"name":"Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Bousquet","sequence":"additional","affiliation":[{"name":"Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8416-3514","authenticated-orcid":false,"given":"Boris","family":"Parra","sequence":"additional","affiliation":[{"name":"Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronom\u00eda, Universidad de las Am\u00e9ricas, Concepci\u00f3n, Chile"},{"name":"Laboratorio de Investigaci\u00f3n de Agentes Antibacterianos (LIAA), Departamento de Microbiolog\u00eda, Facultad de Ciencias Biol\u00f3gicas, Universidad de Concepci\u00f3n, Concepci\u00f3n, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6638-2158","authenticated-orcid":false,"given":"Arnaud","family":"Dechesne","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6227-9906","authenticated-orcid":false,"given":"S\u00f8ren J.","family":"S\u00f8rensen","sequence":"additional","affiliation":[{"name":"Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1929-5040","authenticated-orcid":false,"given":"Joseph","family":"Nesme","sequence":"additional","affiliation":[{"name":"Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1994.1404"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/s0140-6736(69)90163-9"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1128\/jb.110.2.529-537.1972"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.3.2.279"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1017\/s0016672300012179"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1017\/s0016672300014890"},{"key":"R7","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1128\/jb.113.2.772-780.1973","article-title":"Host range and properties of the Pseudomonas aeruginosa R factor R1822","volume":"113","author":"Olsen","year":"1973","journal-title":"J Bacteriol"},{"key":"R8","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1128\/jb.108.3.1244-1249.1971","article-title":"Properties of an R factor from Pseudomonas aeruginosa","volume":"108","author":"Datta","year":"1971","journal-title":"J Bacteriol"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1017\/S0016672300013252"},{"key":"R10","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1099\/00221287-114-2-341","article-title":"Relationship of group P1 plasmids revealed by heteroduplex experiments: RP1, RP4, R68 and RK2 are identical","volume":"114","author":"Burkardt","year":"1979","journal-title":"J Gen Microbiol"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1007\/BF01566742"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1016\/0147-619X(81)90052-4"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1016\/j.plasmid.2007.01.001"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.48.10.3817-3822.2004"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv383"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn322"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0011147"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2289704"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01488-1"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1002\/pro.3943"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msz185"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-12-402"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-017-0242-3"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-017-0243-2"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.01328"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1016\/j.plasmid.2022.102618"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2019.0248"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00380"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-018-0276-9"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.1007\/s10482-009-9316-9"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.05439-11"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1128\/aem.60.3.831-839.1994"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1016\/j.plasmid.2004.09.004"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbiotec.2010.11.018"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msy225"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1007\/BF00272339"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.1016\/j.femsre.2004.10.004"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1007\/pl00006158"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1016\/s1369-5274(00)00188-0"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.2761"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1128\/JB.183.3.1022-1031.2001"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1016\/j.plasmid.2010.06.004"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mss210"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1128\/MRA.01014-20"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1111\/1574-6968.12618"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.950600"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2015.163"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1007\/BF00331014"},{"key":"R54","doi-asserted-by":"publisher","DOI":"10.1126\/science.aba5256"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.1093\/pcp\/pcf175"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460-2075.1985.tb03715.x"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.1128\/jb.174.6.1862-1868.1992"},{"key":"R58","doi-asserted-by":"publisher","DOI":"10.1021\/acs.est.0c03114"},{"key":"R59","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-147-8-2065"},{"key":"R60","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.femsle.2004.10.016","article-title":"Evidence for past integration of incp-1 plasmids into bacterial chromosomes","volume":"241","author":"Chiu","year":"2004","journal-title":"FEMS Microbiol Lett"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001381?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,28]],"date-time":"2025-03-28T12:37:56Z","timestamp":1743165476000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001381"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,28]]},"references-count":60,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,3,28]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001381","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,28]]}}}