{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T00:29:37Z","timestamp":1791937777020,"version":"4.3.4"},"reference-count":57,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,2,26]],"date-time":"2024-02-26T00:00:00Z","timestamp":1708905600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>The emergence of extended-spectrum \u03b2-lactamase (ESBL)-producing Enterobacteriaceae is an urgent and alarming One Health problem. This study aimed to investigate duplications of plasmid-encoded ESBL genes and their impact on antimicrobial resistance (AMR) phenotypes in clinical and screening isolates.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Multi-drug-resistant bacteria from hospitalized patients were collected during routine clinical surveillance from January 2022 to June 2023, and their antimicrobial susceptibility patterns were determined. Genotypes were extracted from long-read whole-genome sequencing data. Furthermore, plasmids and other mobile genetic elements associated with ESBL genes were characterized, and the ESBL genes were correlated to ceftazidime minimal inhibitory concentration (MIC).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In total, we identified four cases of plasmid-encoded ESBL gene duplications that match four genetically similar plasmids during the 18-month surveillance period: five <jats:italic>Escherichia coli<\/jats:italic> and three <jats:italic>Klebsiella pneumoniae<\/jats:italic> isolates. As the ESBL genes were part of transposable elements, the surrounding sequence regions were duplicated as well. In-depth analysis revealed insertion sequence (IS)-mediated transposition mechanisms. Isolates with duplicated ESBL genes exhibited a higher MIC for ceftazidime in comparison to isolates with a single gene copy (3\u2013256 <jats:italic>vs.<\/jats:italic> 1.5\u201332 mg\/L, respectively).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>ESBL gene duplications led to an increased phenotypic resistance against ceftazidime. Our data suggest that ESBL gene duplications by an IS-mediated transposition are a relevant mechanism for how AMR develops in the clinical setting and is part of the microevolution of plasmids.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2024.1343858","type":"journal-article","created":{"date-parts":[[2024,2,26]],"date-time":"2024-02-26T04:51:32Z","timestamp":1708923092000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Plasmid-encoded gene duplications of extended-spectrum \u03b2-lactamases in clinical bacterial isolates"],"prefix":"10.3389","volume":"14","author":[{"given":"Annika","family":"Sobkowiak","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Scherff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franziska","family":"Schuler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Bletz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Mellmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vera","family":"Schwierzeck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"van Almsick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,2,26]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/s41579-021-00650-4","article-title":"Horizontal gene transfer and adaptive evolution in bacteria","volume":"20","author":"Arnold","year":"2022","journal-title":"Nat. Rev. Microbiol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"6281","DOI":"10.1007\/s11033-020-05651-9","article-title":"Metallo-\u00df-lactamases: a review","volume":"47","author":"Behzadi","year":"2020","journal-title":"Mol. Biol. Rep."},{"key":"B3","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1093\/jac\/dkaa399","article-title":"The global prevalence and trend of human intestinal carriage of ESBL-producing Escherichia coli in the community","volume":"76","author":"Bezabih","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"B4","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1128\/CMR.14.4.933-951.2001","article-title":"Extended-spectrum beta-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat","volume":"14","author":"Bradford","year":"2001","journal-title":"Clin. Microbiol. Rev."},{"key":"B5","doi-asserted-by":"publisher","first-page":"e893","DOI":"10.1016\/S2542-5196(21)00280-1","article-title":"Global antibiotic consumption and usage in humans 2000-18: a spatial modelling study","volume":"5","author":"Browne","year":"2021","journal-title":"Lancet Planet Health"},{"key":"B6","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1007\/s00103-012-1549-5","article-title":"Hygienema\u00dfnahmen bei Infektionen oder Besiedlung mit multiresistenten gramnegativen St\u00e4bchen. Empfehlung der Kommission f\u00fcr Krankenhaushygiene und Infektionspr\u00e4vention (KRINKO) beim Robert Koch-Institut (RKI)","volume":"55","year":"2012","journal-title":"Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz"},{"key":"B7","doi-asserted-by":"publisher","first-page":"2227","DOI":"10.1128\/AAC.01707-08","article-title":"Resistance plasmid families in Enterobacteriaceae","volume":"53","author":"Carattoli","year":"2009","journal-title":"Antimicrobial. Agents Chemother."},{"key":"B8","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1016\/j.ijmm.2013.02.001","article-title":"Plasmids and the spread of resistance","volume":"303","author":"Carattoli","year":"2013","journal-title":"Int. J. Med. Microbiol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/aac.02412-14","article-title":"In silico detection and typing of plasmids using plasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrobial. Agents Chemother."},{"key":"B10","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1080\/22221751.2019.1626197","article-title":"Transmission of ciprofloxacin resistance in Salmonella mediated by a novel type of conjugative helper plasmids","volume":"8","author":"Chen","year":"2019","journal-title":"Emerg. Microbes Infect."},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01816-19","article-title":"Ceftazidime-Avibactam Resistance Associated with Increased blaKPC-3 Gene Copy Number Mediated by pKpQIL Plasmid Derivatives in Sequence Type 258 Klebsiella pneumoniae","volume":"64","author":"Coppi","year":"2020","journal-title":"Antimicrobial. Agents Chemother."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"B13","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1038\/208239a0","article-title":"Penicillinase synthesis controlled by infectious R factors in Enterobacteriaceae","volume":"208","author":"Datta","year":"1965","journal-title":"Nature"},{"key":"B14","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1128\/MMBR.00016-10","article-title":"Origins and evolution of antibiotic resistance","volume":"74","author":"Davies","year":"2010","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.001214","article-title":"Evolution of horizontal transmission in antimicrobial resistance plasmids","volume":"168","author":"Dimitriu","year":"2022","journal-title":"Microbiol. (Reading)"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1016\/j.onehlt.2021.100354","article-title":"Prevalence and zoonotic transmission of colistin-resistant and carbapenemase-producing Enterobacterales on German pig farms","volume":"13","author":"Effelsberg","year":"2021","journal-title":"One Health"},{"key":"B17","unstructured":"Breakpoint tables for interpretation of MICs and zone diameters. Version 13.12023"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1128\/aac.00483-19","article-title":"Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates","volume":"63","author":"Feldgarden","year":"2019","journal-title":"Antimicrobial. Agents Chemother."},{"key":"B19","doi-asserted-by":"publisher","first-page":"e672","DOI":"10.1016\/S2666-5247(22)00116-1","article-title":"Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study","volume":"3","author":"Finci","year":"2022","journal-title":"Lancet Microbe"},{"key":"B20","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1038\/nrmicro1235","article-title":"Mobile genetic elements: the agents of open source evolution","volume":"3","author":"Frost","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1111\/j.1469-0691.2009.02790.x","article-title":"The blaSHV-5 gene is encoded in a compound transposon duplicated in tandem in Enterobacter cloacae","volume":"15","author":"Garza-Ramos","year":"2009","journal-title":"Clin. Microbiol. Infect."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.741972","article-title":"Undetectable production of the VIM-1 carbapenemase in an atlantibacter hermannii clinical isolate","volume":"12","author":"Girlich","year":"2021","journal-title":"Front. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.757470","article-title":"Emergence of ceftazidime\/avibactam and tigecycline resistance in carbapenem-resistant klebsiella pneumoniae due to in-host microevolution","volume":"11","author":"Han","year":"2021","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000291","article-title":"An analysis of the IS6\/IS26 family of insertion sequences: IS it a single family","volume":"5","author":"Harmer","year":"2019","journal-title":"Microbial. Genomics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"1428","DOI":"10.1093\/jac\/dkab055","article-title":"IS26 cannot move alone","volume":"76","author":"Harmer","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00762-15","article-title":"Insertion sequence IS26 reorganizes plasmids in clinically isolated multidrug-resistant bacteria by replicative transposition","volume":"6","author":"He","year":"2015","journal-title":"mBio"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.15252\/embr.202051034","article-title":"Antibiotic resistance and persistence-Implications for human health and treatment perspectives","volume":"21","author":"Huemer","year":"2020","journal-title":"EMBO Rep."},{"key":"B28","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1038\/nrg2689","article-title":"The evolution of gene duplications: classifying and distinguishing between models","volume":"11","author":"Innan","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"B29","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder","volume":"76","author":"Johansson","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"B30","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1038\/nbt.2522","article-title":"Updating benchtop sequencing performance comparison","volume":"31","author":"J\u00fcnemann","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"B31","doi-asserted-by":"publisher","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":"B32","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1038\/s12276-021-00569-z","article-title":"Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission","volume":"53","author":"Kim","year":"2021","journal-title":"Exp. Mol. Med."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1435","DOI":"10.1093\/cid\/cix132","article-title":"The hospital water environment as a reservoir for carbapenem-resistant organisms causing hospital-acquired infections\u2014A systematic review of the literature","volume":"64","author":"Kizny Gordon","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01374","article-title":"A review of SHV extended-spectrum \u03b2-lactamases: neglected yet ubiquitous","volume":"7","author":"Liakopoulos","year":"2016","journal-title":"Front. Microbiol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1354","DOI":"10.1038\/s41559-017-0243-2","article-title":"Compensatory mutations improve general permissiveness to antibiotic resistance plasmids","volume":"1","author":"Loftie-Eaton","year":"2017","journal-title":"Nat. Ecol. Evol."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-10210-3","article-title":"TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy","volume":"10","author":"Meier-Kolthoff","year":"2019","journal-title":"Nat. Commun."},{"key":"B37","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis","volume":"399","author":"Murray","year":"2022","journal-title":"Lancet"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00989-17","article-title":"Resistance to ceftazidime-avibactam is due to transposition of KPC in a porin-deficient strain of klebsiella pneumoniae with increased efflux activity","volume":"61","author":"Nelson","year":"2017","journal-title":"Antimicrobial. Agents Chemother."},{"key":"B39","doi-asserted-by":"publisher","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":"B40","article-title":"Antimicrobial resistance: tackling a crisis for the health and wealth of nations 2014","author":"O\u2019Neill","year":"2014","journal-title":"Rev. Antimicrobial. Resist"},{"key":"B41","doi-asserted-by":"publisher","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":"B42","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000206","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microbial. Genomics"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02060-21","article-title":"TnCentral: a prokaryotic transposable element database and web portal for transposon analysis","volume":"12","author":"Ross","year":"2021","journal-title":"mBio"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1128\/microbiolspec.mtbp-0016-2017","article-title":"Fitness costs of plasmids: a limit to plasmid transmission","volume":"5","author":"San Millan","year":"2017","journal-title":"Microbiol. Spectr."},{"key":"B45","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1093\/jac\/dkab407","article-title":"Ultra-deep long-read sequencing detects IS-mediated gene duplications as a potential trigger to generate arrays of resistance genes and a mechanism to induce novel gene variants such as blaCTX-M-243","volume":"77","author":"Schuster","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00476-22","article-title":"Systematic analysis of mobile genetic elements mediating \u03b2-lactamase gene amplification in noncarbapenemase-producing carbapenem-resistant enterobacterales bloodstream infections","volume":"7","author":"Shropshire","year":"2022","journal-title":"mSystems"},{"key":"B47","doi-asserted-by":"publisher","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":"B48","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1016\/S1473-3099(17)30753-3","article-title":"Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis","volume":"18","author":"Tacconelli","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"B49","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1016\/j.jgar.2021.10.004","article-title":"Duplication of blaCTX-M-1 and a class 1 integron on the chromosome enhances antimicrobial resistance in Escherichia coli isolated from racehorses in Japan","volume":"27","author":"Tamamura-Andoh","year":"2021","journal-title":"J. Global Antimicrobial. Resist."},{"key":"B50","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1093\/bioinformatics\/btx713","article-title":"DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication","volume":"34","author":"Tanizawa","year":"2018","journal-title":"Bioinformatics"},{"key":"B51","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/s13100-019-0182-3","article-title":"The transposon registry","volume":"10","author":"Tansirichaiya","year":"2019","journal-title":"Mobile DNA"},{"key":"B52","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1038\/nrmicro1234","article-title":"Mechanisms of, and barriers to, horizontal gene transfer between bacteria","volume":"3","author":"Thomas","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"491","DOI":"10.3390\/microorganisms10030491","article-title":"The Use of Long-Read Sequencing Technologies in Infection Control: Horizontal Transfer of a blaCTX-M-27 Containing lncFII Plasmid in a Patient Screening Sample","volume":"10","author":"van Almsick","year":"2022","journal-title":"Microorganisms"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-021-00239-x","article-title":"The IS6 family, a clinically important group of insertion sequences including IS26","volume":"12","author":"Varani","year":"2021","journal-title":"Mobile DNA"},{"key":"B55","first-page":"277","article-title":"The antibiotic resistance crisis: part 1: causes and threats","volume":"40","author":"Ventola","year":"2015","journal-title":"P T"},{"key":"B56","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/s41559-020-01320-z","article-title":"Timing the origin of eukaryotic cellular complexity with ancient duplications","volume":"5","author":"Vosseberg","year":"2021","journal-title":"Nat. Ecol. Evol."},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.00761","article-title":"Targeting plasmids to limit acquisition and transmission of antimicrobial resistance","volume":"11","author":"Vrancianu","year":"2020","journal-title":"Front. Microbiol."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1343858\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,26]],"date-time":"2024-02-26T04:51:36Z","timestamp":1708923096000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1343858\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,26]]},"references-count":57,"alternative-id":["10.3389\/fcimb.2024.1343858"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2024.1343858","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,26]]},"article-number":"1343858"}}