{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T20:37:46Z","timestamp":1780087066773,"version":"3.54.0"},"reference-count":78,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T00:00:00Z","timestamp":1759276800000},"content-version":"vor","delay-in-days":30,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100011958","name":"Danmarks Frie Forskningsfond","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011958","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004836","name":"Independent Research Fund Denmark","doi-asserted-by":"publisher","award":["3105-00303B"],"award-info":[{"award-number":["3105-00303B"]}],"id":[{"id":"10.13039\/501100004836","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Plasmid"],"published-print":{"date-parts":[[2025,9]]},"DOI":"10.1016\/j.plasmid.2025.102759","type":"journal-article","created":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T06:25:06Z","timestamp":1758695106000},"page":"102759","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"special_numbering":"C","title":["Single-strain mobilome sequencing quantifies bacterial genetic response to stress, including activity of IS elements, prophages, RNAs, and REPINs."],"prefix":"10.1016","volume":"134","author":[{"given":"Tue Kj\u00e6rgaard","family":"Nielsen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars Hestbjerg","family":"Hansen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.plasmid.2025.102759_bb0005","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.3390\/microorganisms10091793","article-title":"Gene networks and pathways involved in Escherichia coli response to multiple stressors","volume":"10","author":"Abdelwahed","year":"2022","journal-title":"Microorganisms"},{"key":"10.1016\/j.plasmid.2025.102759_bb0010","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1128\/jb.173.1.229-233.1991","article-title":"Detergent (sodium dodecyl sulfate) shock proteins in Escherichia coli","volume":"173","author":"Adamowicz","year":"1991","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0015","doi-asserted-by":"crossref","first-page":"6133","DOI":"10.1128\/JB.186.18.6133-6141.2004","article-title":"An SOS response induced by high pressure in Escherichia coli","volume":"186","author":"Aertsen","year":"2004","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0020","doi-asserted-by":"crossref","DOI":"10.1016\/j.plasmid.2021.102576","article-title":"An improved direct metamobilome approach increases the detection of larger-sized circular elements across kingdoms","volume":"115","author":"Alanin","year":"2021","journal-title":"Plasmid"},{"key":"10.1016\/j.plasmid.2025.102759_bb0025","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0030","doi-asserted-by":"crossref","first-page":"2438","DOI":"10.1128\/AAC.01549-10","article-title":"Vibrio cholerae triggers SOS and mutagenesis in response to a wide range of antibiotics: a route towards multiresistance","volume":"55","author":"Baharoglu","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.plasmid.2025.102759_bb0035","doi-asserted-by":"crossref","first-page":"27622","DOI":"10.1074\/jbc.M201978200","article-title":"The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids","volume":"277","author":"Balandina","year":"2002","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.plasmid.2025.102759_bb0040","doi-asserted-by":"crossref","first-page":"18777","DOI":"10.1038\/s41598-019-55332-2","article-title":"Transcriptional and translational inhibitors block SOS response and Shiga toxin expression in enterohemorrhagic Escherichia coli","volume":"9","author":"Berger","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.plasmid.2025.102759_bb0045","doi-asserted-by":"crossref","DOI":"10.1002\/bies.202200085","article-title":"Ancient Darwinian replicators nested within eubacterial genomes","volume":"45","author":"Bertels","year":"2023","journal-title":"BioEssays"},{"key":"10.1016\/j.plasmid.2025.102759_bb0050","doi-asserted-by":"crossref","first-page":"2110","DOI":"10.1093\/gbe\/evx146","article-title":"Identification and characterization of domesticated bacterial transposases","volume":"9","author":"Bertels","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0055","doi-asserted-by":"crossref","first-page":"8788","DOI":"10.1038\/s41598-022-12463-3","article-title":"Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors","volume":"12","author":"Bhatia","year":"2022","journal-title":"Sci. Rep."},{"key":"10.1016\/j.plasmid.2025.102759_bb0060","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0224650","article-title":"The mutational landscape of quinolone resistance in Escherichia coli","volume":"14","author":"Bhatnagar","year":"2019","journal-title":"PLoS One"},{"key":"10.1016\/j.plasmid.2025.102759_bb0065","doi-asserted-by":"crossref","first-page":"5863","DOI":"10.1093\/nar\/19.21.5863","article-title":"A novel RNA product of the tyrT operon of Escherichia Coli","volume":"19","author":"B\u00f6sl","year":"1991","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.plasmid.2025.102759_bb0070","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/j.mimet.2013.09.008","article-title":"A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches","volume":"95","author":"Brown Kav","year":"2013","journal-title":"J. Microbiol. Methods"},{"key":"10.1016\/j.plasmid.2025.102759_bb0075","series-title":"The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements","author":"Browne","year":"2020"},{"key":"10.1016\/j.plasmid.2025.102759_bb0080","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa008","article-title":"GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms","volume":"9","author":"Browne","year":"2020","journal-title":"Gigascience"},{"key":"10.1016\/j.plasmid.2025.102759_bb0085","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1146\/annurev-chembioeng-101121-070250","article-title":"RNAs as sensors of oxidative stress in Bacteria","volume":"14","author":"Buchser","year":"2023","journal-title":"Annu. Rev. Chem. Biomol. Eng."},{"key":"10.1016\/j.plasmid.2025.102759_bb0090","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s12866-020-1721-2","article-title":"Genome-wide identification for genes involved in sodium dodecyl sulfate toxicity in Saccharomyces cerevisiae","volume":"20","author":"Cao","year":"2020","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0095","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1111\/mmi.15140","article-title":"The insertion sequence excision enhancer: a PrimPol-based primer invasion system for immobilizing transposon-transmitted antibiotic resistance genes","volume":"120","author":"Chandler","year":"2023","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0100","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1038\/s41467-021-21210-7","article-title":"Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria","volume":"12","author":"Consuegra","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.plasmid.2025.102759_bb0105","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1038\/nrm1241","article-title":"The outs and ins of transposition: from mu to kangaroo","volume":"4","author":"Curcio","year":"2003","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0110","doi-asserted-by":"crossref","first-page":"3512","DOI":"10.1128\/AEM.71.7.3512-3518.2005","article-title":"Role of porins in sensitivity of Escherichia coli to antibacterial activity of the Lactoperoxidase enzyme system","volume":"71","author":"De Spiegeleer","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0115","doi-asserted-by":"crossref","first-page":"2886","DOI":"10.1073\/pnas.1919800117","article-title":"RNA sequencing by direct tagmentation of RNA\/DNA hybrids","volume":"117","author":"Di","year":"2020","journal-title":"Proc. Natl. Acad. Sci."},{"key":"10.1016\/j.plasmid.2025.102759_bb0120","doi-asserted-by":"crossref","first-page":"2415","DOI":"10.1038\/s41396-023-01547-1","article-title":"Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria","volume":"17","author":"Dougherty","year":"2023","journal-title":"ISME J."},{"key":"10.1016\/j.plasmid.2025.102759_bb0125","doi-asserted-by":"crossref","first-page":"5809","DOI":"10.1128\/AAC.03364-14","article-title":"Transient and sustained bacterial adaptation following repeated sublethal exposure to microbicides and a novel human antimicrobial peptide","volume":"58","author":"Forbes","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.plasmid.2025.102759_bb0130","doi-asserted-by":"crossref","DOI":"10.24072\/pcjournal.244","article-title":"RAREFAN: a webservice to identify REPINs and RAYTs in bacterial genomes","volume":"3","author":"Fortmann-Grote","year":"2023","journal-title":"Peer Commun. J."},{"key":"10.1016\/j.plasmid.2025.102759_bb0135","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2022.118740","article-title":"Identifying the mediators of intracellular E. coli inactivation under UVA light: the (photo) Fenton process and singlet oxygen","volume":"221","author":"Giannakis","year":"2022","journal-title":"Water Res."},{"key":"10.1016\/j.plasmid.2025.102759_bb0140","doi-asserted-by":"crossref","first-page":"11685","DOI":"10.1074\/jbc.REV119.005593","article-title":"Trouble is coming: Signaling pathways that regulate general stress responses in bacteria","volume":"294","author":"Gottesman","year":"2019","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.plasmid.2025.102759_bb0145","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1128\/jb.144.1.312-321.1980","article-title":"Identification of a novel genetic element in Escherichia coli K-12","volume":"144","author":"Greener","year":"1980","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0150","first-page":"5","article-title":"Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals","author":"Gullberg","year":"2014","journal-title":"mBio"},{"key":"10.1016\/j.plasmid.2025.102759_bb0155","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0019912","article-title":"Design and synthesis of a quintessential self-transmissible IncX1 plasmid, pX1.0","volume":"6","author":"Hansen","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.plasmid.2025.102759_bb0160","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0180156","article-title":"Hopping into a hot seat: role of DNA structural features on IS5-mediated gene activation and inactivation under stress","volume":"12","author":"Humayun","year":"2017","journal-title":"PLoS One"},{"key":"10.1016\/j.plasmid.2025.102759_bb0165","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0087924","article-title":"Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome","author":"J\u00f8rgensen","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.plasmid.2025.102759_bb0170","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1093\/nar\/gkac004","article-title":"Experimental demonstration of operon formation catalyzed by insertion sequence","volume":"50","author":"Kanai","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.plasmid.2025.102759_bb0175","doi-asserted-by":"crossref","first-page":"1520","DOI":"10.4161\/rna.22757","article-title":"Divergently overlapping cis -encoded antisense RNA regulating toxin-antitoxin systems from E. coli","volume":"9","author":"Kawano","year":"2012","journal-title":"RNA Biol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0180","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.711077","article-title":"The EcoCyc database in 2021","volume":"12","author":"Keseler","year":"2021","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0185","doi-asserted-by":"crossref","first-page":"7032","DOI":"10.1073\/pnas.1300627110","article-title":"Rhs proteins from diverse bacteria mediate intercellular competition","volume":"110","author":"Koskiniemi","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.plasmid.2025.102759_bb0190","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013","journal-title":"ArXiv"},{"key":"10.1016\/j.plasmid.2025.102759_bb0195","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.plasmid.2025.102759_bb0200","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1080\/15476286.2015.1112489","article-title":"REP sequences: mediators of the environmental stress response?","volume":"13","author":"Liang","year":"2016","journal-title":"RNA Biol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0205","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2022.160516","article-title":"Oxidative stress induced by sub-lethal exposure to copper as a mediator in development of bacterial resistance to antibiotics","volume":"860","author":"Liu","year":"2023","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.plasmid.2025.102759_bb0210","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.142702","article-title":"Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments","volume":"755","author":"Mazhar","year":"2021","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.plasmid.2025.102759_bb0215","doi-asserted-by":"crossref","first-page":"9964","DOI":"10.1093\/nar\/gks741","article-title":"The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease","volume":"40","author":"Messing","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.plasmid.2025.102759_bb0220","doi-asserted-by":"crossref","first-page":"8438","DOI":"10.1038\/s41598-020-64995-1","article-title":"Global responses to oxytetracycline treatment in tetracycline-resistant Escherichia coli","volume":"10","author":"M\u00f8ller","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.plasmid.2025.102759_bb0225","doi-asserted-by":"crossref","first-page":"21","DOI":"10.4315\/0362-028X-72.1.21","article-title":"Integron-mediated antibiotic resistance in Shiga toxin\u2013producing Escherichia coli","volume":"72","author":"Nagachinta","year":"2009","journal-title":"J. Food Prot."},{"key":"10.1016\/j.plasmid.2025.102759_bb0230","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.gene.2005.04.029","article-title":"Genetic analysis of the requirements for SOS induction by nalidixic acid in Escherichia coli","volume":"356","author":"Newmark","year":"2005","journal-title":"Gene"},{"key":"10.1016\/j.plasmid.2025.102759_bb0235","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0083346","article-title":"Novel insight into the genetic context of the cadAB genes from a 4-chloro-2-methylphenoxyacetic acid-degrading Sphingomonas","author":"Nielsen","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.plasmid.2025.102759_bb0240","doi-asserted-by":"crossref","DOI":"10.1093\/gbe\/evx185","article-title":"Evolution of sphingomonad gene clusters related to pesticide catabolism revealed by genome sequence and mobilomics of Sphingobium herbicidovorans MH","author":"Nielsen","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0245","doi-asserted-by":"crossref","first-page":"18943","DOI":"10.1038\/s41598-021-98184-5","article-title":"The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids","volume":"11","author":"Nielsen","year":"2021","journal-title":"Sci. Rep."},{"key":"10.1016\/j.plasmid.2025.102759_bb0250","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giac072","article-title":"Antibiotic resistance genes are differentially mobilized according to resistance mechanism","volume":"11","author":"Nielsen","year":"2022","journal-title":"Gigascience"},{"key":"10.1016\/j.plasmid.2025.102759_bb0255","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.plasmid.2008.03.003","article-title":"Nucleotide sequence of pOLA52: a conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux","volume":"60","author":"Norman","year":"2008","journal-title":"Plasmid"},{"key":"10.1016\/j.plasmid.2025.102759_bb0260","series-title":"Metal Resistance and Its Association With Antibiotic Resistance","first-page":"261","author":"Pal","year":"2017"},{"key":"10.1016\/j.plasmid.2025.102759_bb0265","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/CMR.00088-17","article-title":"Mobile genetic elements associated with antimicrobial resistance","volume":"31","author":"Partridge","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.plasmid.2025.102759_bb0270","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1534\/g3.114.015933","article-title":"Insights into ongoing evolution of the hexachlorocyclohexane catabolic pathway from comparative genomics of ten Sphingomonadaceae strains","volume":"5","author":"Pearce","year":"2015","journal-title":"G3 Genes|Genomes|Genetics"},{"key":"10.1016\/j.plasmid.2025.102759_bb0275","doi-asserted-by":"crossref","DOI":"10.1016\/j.bpc.2023.107040","article-title":"The membrane-binding bacterial toxin long direct repeat D inhibits protein translation","volume":"298","author":"Pulido","year":"2023","journal-title":"Biophys. Chem."},{"key":"10.1016\/j.plasmid.2025.102759_bb0280","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1007\/s00294-016-0654-7","article-title":"DNA repeat sequences: diversity and versatility of functions","volume":"63","author":"Qian","year":"2017","journal-title":"Curr. Genet."},{"key":"10.1016\/j.plasmid.2025.102759_bb0285","first-page":"6","article-title":"A new noncoding RNA arranges bacterial chromosome organization","author":"Qian","year":"2015","journal-title":"mBio"},{"key":"10.1016\/j.plasmid.2025.102759_bb0290","doi-asserted-by":"crossref","first-page":"4117","DOI":"10.1128\/AEM.68.8.4117-4121.2002","article-title":"Sodium dodecyl Sulfate hypersensitivity of clpP and clpB mutants of Escherichia coli","volume":"68","author":"Rajagopal","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0295","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1186\/s12934-016-0577-5","article-title":"Genome-wide Escherichia coli stress response and improved tolerance towards industrially relevant chemicals","volume":"15","author":"Rau","year":"2016","journal-title":"Microb. Cell Factories"},{"key":"10.1016\/j.plasmid.2025.102759_bb0300","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the national center for biotechnology information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.plasmid.2025.102759_bb0305","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2021.821535","article-title":"Bacterial response to oxidative stress and RNA oxidation","volume":"12","author":"Seixas","year":"2022","journal-title":"Front. Genet."},{"key":"10.1016\/j.plasmid.2025.102759_bb0310","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S0378-1119(97)00057-7","article-title":"Isolation and characterization of IS1 circles","volume":"191","author":"Sekine","year":"1997","journal-title":"Gene"},{"key":"10.1016\/j.plasmid.2025.102759_bb0315","doi-asserted-by":"crossref","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: the reference Centre for bacterial insertion sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.plasmid.2025.102759_bb0320","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1111\/1574-6976.12067","article-title":"Bacterial insertion sequences: their genomic impact and diversity","volume":"38","author":"Siguier","year":"2014","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.plasmid.2025.102759_bb0325","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/0147-619X(85)90008-3","article-title":"DNA segments of the IncX plasmid R485 determining replication and incompatibility with plasmid R6K","volume":"14","author":"Stalker","year":"1985","journal-title":"Plasmid"},{"key":"10.1016\/j.plasmid.2025.102759_bb0330","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2019.00159","article-title":"Nucleoid-associated protein HU: a lilliputian in gene regulation of bacterial virulence","volume":"9","author":"Stojkova","year":"2019","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0335","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1016\/j.copbio.2015.03.018","article-title":"Quaternary ammonium disinfectants: microbial adaptation, degradation and ecology","volume":"33","author":"Tezel","year":"2015","journal-title":"Curr. Opin. Biotechnol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0340","doi-asserted-by":"crossref","first-page":"3596","DOI":"10.1093\/nar\/gkr1198","article-title":"Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences \u2020","volume":"40","author":"Ton-Hoang","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.plasmid.2025.102759_bb0345","doi-asserted-by":"crossref","first-page":"5410","DOI":"10.1002\/j.1460-2075.1995.tb00225.x","article-title":"IS1-mediated intramolecular rearrangements: formation of excised transposon circles and replicative deletions","volume":"14","author":"Turlan","year":"1995","journal-title":"EMBO J."},{"key":"10.1016\/j.plasmid.2025.102759_bb0350","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1002\/bit.21611","article-title":"The bactericidal effect of ultraviolet and visible light on Escherichia coli","volume":"99","author":"Vermeulen","year":"2008","journal-title":"Biotechnol. Bioeng."},{"key":"10.1016\/j.plasmid.2025.102759_bb0355","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1038\/ncomms1146","article-title":"Cryptic prophages help bacteria cope with adverse environments","volume":"1","author":"Wang","year":"2010","journal-title":"Nat. Commun."},{"key":"10.1016\/j.plasmid.2025.102759_bb0360","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.137055","article-title":"Heavy metal copper accelerates the conjugative transfer of antibiotic resistance genes in freshwater microcosms","volume":"717","author":"Wang","year":"2020","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.plasmid.2025.102759_bb0365","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1046\/j.1365-2958.2000.01805.x","article-title":"Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, topoisomerase I and Fis","volume":"35","author":"Weinstein-Fischer","year":"2000","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0370","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1146\/annurev-micro-032521-022006","article-title":"Mobile genetic element flexibility as an underlying principle to bacterial evolution","volume":"77","author":"Weisberg","year":"2023","journal-title":"Ann. Rev. Microbiol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0375","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/j.yrtph.2013.09.006","article-title":"Modes of action of three disinfectant active substances: a review","volume":"67","author":"Wessels","year":"2013","journal-title":"Regul. Toxicol. Pharmacol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0380","series-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"10.1016\/j.plasmid.2025.102759_bb0385","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1159\/000357949","article-title":"Characterization of LdrA (Long direct repeat A) protein of Escherichia coli","volume":"24","author":"Yamaguchi","year":"2014","journal-title":"Microb. Physiol."},{"key":"10.1016\/j.plasmid.2025.102759_bb0390","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1016\/j.scitotenv.2018.11.372","article-title":"Evidence for co-selection of antibiotic resistance genes and mobile genetic elements in metal polluted urban soils","volume":"656","author":"Zhao","year":"2019","journal-title":"Sci. Total Environ."}],"container-title":["Plasmid"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0147619X25000174?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0147619X25000174?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T08:55:15Z","timestamp":1773132915000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0147619X25000174"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9]]},"references-count":78,"alternative-id":["S0147619X25000174"],"URL":"https:\/\/doi.org\/10.1016\/j.plasmid.2025.102759","relation":{},"ISSN":["0147-619X"],"issn-type":[{"value":"0147-619X","type":"print"}],"subject":[],"published":{"date-parts":[[2025,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Single-strain mobilome sequencing quantifies bacterial genetic response to stress, including activity of IS elements, prophages, RNAs, and REPINs.","name":"articletitle","label":"Article Title"},{"value":"Plasmid","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.plasmid.2025.102759","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"102759"}}