{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T13:03:02Z","timestamp":1790254982955,"version":"4.1.0"},"reference-count":56,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":8,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":["cell.com","clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Trends in Microbiology"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.tim.2026.09.002","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T11:25:04Z","timestamp":1790249104000},"update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Plasmid typing challenges in the era of genomic antimicrobial resistance surveillance"],"prefix":"10.1016","author":[{"given":"Gijs","family":"Teunis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louise","family":"Roer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anita C.","family":"Sch\u00fcrch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lapo","family":"Mughini-Gras","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4431-9323","authenticated-orcid":false,"given":"Antoni P.A.","family":"Hendrickx","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.tim.2026.09.002_bb0005","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1016\/S1473-3099(25)00118-5","article-title":"The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance","volume":"25","author":"Sati","year":"2025","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.tim.2026.09.002_bb0010","first-page":"1199","article-title":"Antimicrobial Resistance Collaborators (2024) Global burden of bacterial antimicrobial resistance 1990\u20132021: a systematic analysis with forecasts to 2050","volume":"404","author":"GBD","year":"2021","journal-title":"Lancet"},{"key":"10.1016\/j.tim.2026.09.002_bb0015","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/s41579-020-00497-1","article-title":"Beyond horizontal gene transfer: the role of plasmids in bacterial evolution","volume":"19","author":"Rodr\u00edguez-beltr\u00e1n","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.tim.2026.09.002_bb0020","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.3389\/fmicb.2020.02033","article-title":"Plasmid interactions can improve plasmid persistence in bacterial populations","volume":"11","author":"Gama","year":"2020","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.tim.2026.09.002_bb0025","doi-asserted-by":"crossref","first-page":"2653","DOI":"10.1038\/s41467-021-22849-y","article-title":"Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities","volume":"12","author":"Valle","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.tim.2026.09.002_bb0030","first-page":"10","article-title":"Fitness costs of plasmids: a limit to plasmid transmission","volume":"5","author":"Millan","year":"2017","journal-title":"Microbiol. Spectrum"},{"key":"10.1016\/j.tim.2026.09.002_bb0035","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.03191-22","article-title":"Plasmid-encoded traits vary across environments","volume":"14","author":"Finks","year":"2023","journal-title":"MBio"},{"key":"10.1016\/j.tim.2026.09.002_bb0040","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1139\/cjm-2018-0275","article-title":"Horizontal transfer of antibiotic resistance genes in clinical environments","volume":"65","author":"Lerminiaux","year":"2019","journal-title":"Can. J. Microbiol."},{"key":"10.1016\/j.tim.2026.09.002_bb0045","doi-asserted-by":"crossref","first-page":"173","DOI":"10.3389\/fmicb.2016.00173","article-title":"Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer","volume":"7","author":"von Wintersdorff","year":"2016","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.tim.2026.09.002_bb0050","first-page":"47","article-title":"Plasmid copy number and plasmid stability","volume":"86","author":"Friehs","year":"2004","journal-title":"Adv. Biochem. Eng. Biotechnol."},{"key":"10.1016\/j.tim.2026.09.002_bb0055","doi-asserted-by":"crossref","first-page":"2227","DOI":"10.1128\/AAC.01707-08","article-title":"Resistance plasmid families in Enterobacteriaceae","volume":"53","author":"Carattoli","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.tim.2026.09.002_bb0060","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0040438","article-title":"A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings","volume":"7","author":"Alvarado","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.tim.2026.09.002_bb0065","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1128\/MMBR.00020-10","article-title":"Mobility of plasmids","volume":"74","author":"Smillie","year":"2010","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.tim.2026.09.002_bb0070","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.tim.2026.09.002_bb0075","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2212147120","article-title":"Host-specific plasmid evolution explains the variable spread of clinical antibiotic-resistance plasmids","volume":"120","author":"Benz","year":"2023","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.tim.2026.09.002_bb0080","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/s41579-023-00926-x","article-title":"Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era","volume":"22","author":"Casta\u00f1eda-Barba","year":"2024","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.tim.2026.09.002_bb0085","doi-asserted-by":"crossref","first-page":"598","DOI":"10.3390\/microorganisms9030598","article-title":"Outcome of different sequencing and assembly approaches on the detection of plasmids and localization of antimicrobial resistance genes in commensal Escherichia coli","volume":"9","author":"Juraschek","year":"2021","journal-title":"Microorganisms"},{"key":"10.1016\/j.tim.2026.09.002_bb0090","article-title":"Oxford nanopore long-read sequencing enables the generation of complete bacterial and plasmid genomes without short-read sequencing","volume":"14","author":"Zhao","year":"2023","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.tim.2026.09.002_bb0095","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1016\/j.humimm.2021.02.012","article-title":"Next-generation sequencing technologies: an overview","volume":"82","author":"Hu","year":"2021","journal-title":"Hum. Immunol."},{"key":"10.1016\/j.tim.2026.09.002_bb0100","article-title":"On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data","volume":"3","author":"Arredondo-Alonso","year":"2017","journal-title":"Microb. Genom."},{"key":"10.1016\/j.tim.2026.09.002_bb0105","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.tim.2026.09.002_bb0110","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1186\/s13073-024-01412-6","article-title":"Genomic surveillance of multidrug-resistant organisms based on long-read sequencing","volume":"16","author":"Landman","year":"2024","journal-title":"Genome Med."},{"key":"10.1016\/j.tim.2026.09.002_bb0115","doi-asserted-by":"crossref","first-page":"182","DOI":"10.3389\/fmicb.2017.00182","article-title":"Plasmid classification in an era of whole-genome sequencing: application in studies of antibiotic resistance epidemiology","volume":"8","author":"Orlek","year":"2017","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.tim.2026.09.002_bb0120","doi-asserted-by":"crossref","DOI":"10.1016\/j.plasmid.2023.102684","article-title":"Plasmid classifications","volume":"126","author":"Garcill\u00e1n-Barcia","year":"2023","journal-title":"Plasmid"},{"key":"10.1016\/j.tim.2026.09.002_bb0125","doi-asserted-by":"crossref","first-page":"3767","DOI":"10.1128\/AAC.00464-16","article-title":"Nested Russian doll-like genetic mobility drives rapid dissemination of the carbapenem resistance gene blaKPC","volume":"60","author":"Sheppard","year":"2016","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.tim.2026.09.002_bb0130","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btag574","article-title":"pLAST-a tool for rapid comparison and classification of bacterial plasmid sequences","volume":"42","author":"Krakowski","year":"2026","journal-title":"Bioinformatics"},{"key":"10.1016\/j.tim.2026.09.002_bb0135","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1186\/s12859-021-04299-x","article-title":"COPLA, a taxonomic classifier of plasmids","volume":"22","author":"Redondo-Salvo","year":"2021","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.tim.2026.09.002_bb0140","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genom."},{"key":"10.1016\/j.tim.2026.09.002_bb0145","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad612","article-title":"SHIP: identifying antimicrobial resistance gene transfer between plasmids","volume":"39","author":"Teixeira","year":"2023","journal-title":"Bioinformatics"},{"key":"10.1016\/j.tim.2026.09.002_bb0150","article-title":"Mge-cluster: a reference-free approach for typing bacterial plasmids","volume":"5","author":"Arredondo-Alonso","year":"2023","journal-title":"NAR Genom. Bioinform."},{"key":"10.1016\/j.tim.2026.09.002_bb0155","article-title":"Applying rearrangement distances to enable plasmid epidemiology with pling","volume":"10","author":"Frolova","year":"2024","journal-title":"Microb. Genom."},{"key":"10.1016\/j.tim.2026.09.002_bb0160","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1007\/978-1-4939-9877-7_20","article-title":"PlasmidFinder and in silico pMLST: identification and typing of Plasmid replicons in whole-genome sequencing (WGS)","volume":"2075","author":"Carattoli","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.tim.2026.09.002_bb0165","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.plasmid.2015.04.009","article-title":"IncI shufflons: assembly issues in the next-generation sequencing era","volume":"80","author":"Brouwer","year":"2015","journal-title":"Plasmid"},{"key":"10.1016\/j.tim.2026.09.002_bb0170","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.3009845","article-title":"Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae","volume":"6","author":"Conlan","year":"2014","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.tim.2026.09.002_bb0175","doi-asserted-by":"crossref","first-page":"4099","DOI":"10.1021\/acssynbio.4c00539","article-title":"Sequencing strategy to ensure accurate plasmid assembly","volume":"13","author":"Hernandez","year":"2024","journal-title":"ACS Synth. Biol."},{"key":"10.1016\/j.tim.2026.09.002_bb0180","article-title":"Long-read sequencing for bacterial plasmid analysis: a brief overview","volume":"373","author":"van Almsick","year":"2026","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.tim.2026.09.002_bb0185","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1010905","article-title":"Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing","volume":"19","author":"Wick","year":"2023","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.tim.2026.09.002_bb0190","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btaf474","article-title":"Autocycler: long-read consensus assembly for bacterial genomes","volume":"41","author":"Wick","year":"2025","journal-title":"Bioinformatics"},{"key":"10.1016\/j.tim.2026.09.002_bb0195","article-title":"Towards quantifying plasmid similarity","volume":"10","author":"Matlock","year":"2024","journal-title":"Microb. Genom."},{"key":"10.1016\/j.tim.2026.09.002_bb0200","doi-asserted-by":"crossref","DOI":"10.1128\/aac.01097-25","article-title":"Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations","volume":"69","author":"Beh","year":"2025","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.tim.2026.09.002_bb0205","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1073\/pnas.95.6.3140","article-title":"Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms","volume":"95","author":"Maiden","year":"1998","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.tim.2026.09.002_bb0210","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1038\/nrmicro3093","article-title":"MLST revisited: the gene-by-gene approach to bacterial genomics","volume":"11","author":"Maiden","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.tim.2026.09.002_bb0215","series-title":"Methods in Microbiology. Volume 41: New Approaches to Prokaryotic Systematics","first-page":"103","article-title":"Whole-genome analyses: Average Nucleotide Identity","author":"Arahal","year":"2014"},{"key":"10.1016\/j.tim.2026.09.002_bb0220","series-title":"The Prokaryotes","year":"2006"},{"key":"10.1016\/j.tim.2026.09.002_bb0225","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/s41576-025-00911-5","article-title":"Average nucleotide identity \u2013 the backbone of modern ecological genomics","volume":"27","author":"Orellana","year":"2026","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.tim.2026.09.002_bb0230","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.tim.2026.09.002_bb0235","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1093\/bib\/bbz010","article-title":"The global dissemination of bacterial infections necessitates the study of reverse genomic epidemiology","volume":"21","author":"Ruan","year":"2020","journal-title":"Brief. Bioinform."},{"key":"10.1016\/j.tim.2026.09.002_bb0240","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1016\/j.cmi.2017.12.016","article-title":"Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches","volume":"24","author":"Sch\u00fcrch","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"10.1016\/j.tim.2026.09.002_bb0245","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1001165","article-title":"Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation","volume":"6","author":"Baharoglu","year":"2010","journal-title":"PLoS Genet."},{"key":"10.1016\/j.tim.2026.09.002_bb0250","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.plasmid.2019.02.003","article-title":"Mosaic plasmids are abundant and unevenly distributed across prokaryotic taxa","volume":"102","author":"Pesesky","year":"2019","journal-title":"Plasmid"},{"key":"10.1016\/j.tim.2026.09.002_bb0255","doi-asserted-by":"crossref","first-page":"242","DOI":"10.3389\/fmicb.2015.00242","article-title":"Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy","volume":"6","author":"Shintani","year":"2015","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.tim.2026.09.002_bb0260","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0291492","article-title":"Fast genome-based delimitation of Enterobacterales species","volume":"18","author":"Hern\u00e1ndez-Salmer\u00f3n","year":"2023","journal-title":"PLoS One"},{"key":"10.1016\/j.tim.2026.09.002_bb0265","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.tim.2026.09.002_bb0270","article-title":"Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microb. Genom."},{"key":"10.1016\/j.tim.2026.09.002_bb0275","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.tim.2026.09.002_bb0280","doi-asserted-by":"crossref","first-page":"D1020","DOI":"10.1093\/nar\/gkaa1105","article-title":"RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation","volume":"49","author":"Li","year":"2021","journal-title":"Nucleic Acids Res."}],"container-title":["Trends in Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0966842X26002544?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0966842X26002544?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T12:27:48Z","timestamp":1790252868000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0966842X26002544"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":56,"alternative-id":["S0966842X26002544"],"URL":"https:\/\/doi.org\/10.1016\/j.tim.2026.09.002","relation":{},"ISSN":["0966-842X"],"issn-type":[{"value":"0966-842X","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Plasmid typing challenges in the era of genomic antimicrobial resistance surveillance","name":"articletitle","label":"Article Title"},{"value":"Trends in Microbiology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.tim.2026.09.002","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}]}}