{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T18:49:28Z","timestamp":1790189368516,"version":"4.1.0"},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2023,11,16]],"date-time":"2023-11-16T00:00:00Z","timestamp":1700092800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"\n Carbapanem-resistant\n Klebsiella pneumoniae<\/jats:italic>\n is a globally healthcare crisis. The distribution of plasmids carrying carbapenemase genes among\n K<\/jats:italic>\n .\n pneumoniae<\/jats:italic>\n poses a serious threat in clinical settings. Here, we characterized the genetic structure of plasmids harboring major carbapenemases (e.g.\n bla<\/jats:italic>\n KPC<\/jats:sub>\n ,\n bla<\/jats:italic>\n NDM<\/jats:sub>\n ,\n bla<\/jats:italic>\n OXA-48<\/jats:sub>\n -like\n ,<\/jats:sub>\n and\n bla<\/jats:italic>\n GES<\/jats:sub>\n ) from\n K<\/jats:italic>\n .\n pneumoniae<\/jats:italic>\n using bioinformatics tools. The plasmids carrying at least one major carbapenemase gene were retrieved from the GenBank database. The DNA length, Inc type, and conjugal apparatus of these plasmids were detected. Additionally, allele types, co-existence, co-occurrence of carbapenemase genes, gene repetition, and sequence types of isolates, were characterized. There were 2254 plasmids harboring carbapenemase genes in the database. This study revealed that\n bla<\/jats:italic>\n KPC-2<\/jats:sub>\n ,\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n ,\n bla<\/jats:italic>\n OXA-48<\/jats:sub>\n , and\n bla<\/jats:italic>\n GES-5<\/jats:sub>\n were the most prevalent allele types. Out of 1140 (50%) plasmids were potentially conjugative. IncFII, IncR, IncX3, and IncL replicon types were predominant. The co-existence analysis revealed that the most prevalent of other resistance genes were\n bla<\/jats:italic>\n TEM-1<\/jats:sub>\n (related to\n bla<\/jats:italic>\n KPC<\/jats:sub>\n ),\n bla<\/jats:italic>\n OXA-232<\/jats:sub>\n (related to\n bla<\/jats:italic>\n OXA-48<\/jats:sub>\n ),\n ble<\/jats:italic>\n MBL<\/jats:sub>\n (related to\n bla<\/jats:italic>\n NDM<\/jats:sub>\n ), and\n aac (6\u2032)-Ib4<\/jats:italic>\n (related to\n bla<\/jats:italic>\n GES<\/jats:sub>\n ). The co-occurrence of carbapenemases was detected in 42 plasmids while 15 plasmids contained carbapenemase gene repetitions. Sequence alignments highlighted that plasmids carrying\n bla<\/jats:italic>\n KPC<\/jats:sub>\n and\n bla<\/jats:italic>\n OXA-48<\/jats:sub>\n -like were more homogeneous whereas the plasmids carrying\n bla<\/jats:italic>\n NDM<\/jats:sub>\n were divergent. It seems that\n K<\/jats:italic>\n .\n pneumoniae<\/jats:italic>\n utilizes diversity of genetic flexibility and recombination for resistance against carbapenems. The genetic structure of the plasmids showed that class I and III, Tn3 family, Tn5403 family derivatives, and Tn7-like elements were strongly associated with carbapenemases. The mobilizable plasmids carrying carbapenemases play an important role in the spread of these genes. In addition, gene repetition maybe is related to carbapenem heteroresistance. According to MST (minimum spanning tree) results, the majority of plasmids belonged to sequence type (ST) 11, ST14, and ST12. These international clones have a high capacity to acquire the carbapenemase-containing plasmids.\n <\/jats:p>","DOI":"10.1371\/journal.pone.0292288","type":"journal-article","created":{"date-parts":[[2023,11,16]],"date-time":"2023-11-16T13:29:54Z","timestamp":1700141394000},"page":"e0292288","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":20,"title":["Decoding the genetic structure of conjugative plasmids in international clones of Klebsiella pneumoniae: A deep dive into blaKPC, blaNDM, blaOXA-48, and blaGES genes"],"prefix":"10.1371","volume":"18","author":[{"given":"Shadi","family":"Aghamohammad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahshid","family":"Khazani Asforooshani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yeganeh","family":"Malek Mohammadi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Sholeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3502-147X","authenticated-orcid":true,"given":"Farzad","family":"Badmasti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,11,16]]},"reference":[{"key":"pone.0292288.ref001","first-page":"1","article-title":"Molecular characterization of Klebsiella pneumoniae isolates from stool specimens of outpatients in sentinel hospitals Beijing, China, 2010\u20132015","volume":"9","author":"B Lu","year":"2017","journal-title":"Gut pathogens"},{"issue":"3","key":"pone.0292288.ref002","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1089\/mdr.2018.0181","article-title":"First report of extended-spectrum 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Microbiology"},{"key":"pone.0292288.ref005","first-page":"1","article-title":"Systematic review and meta-analysis of mortality of patients infected with carbapenem-resistant Klebsiella pneumoniae","volume":"16","author":"L Xu","year":"2017","journal-title":"Annals of clinical microbiology and antimicrobials"},{"issue":"11","key":"pone.0292288.ref006","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1017\/ice.2017.197","article-title":"Carbapenem resistance, initial antibiotic therapy, and mortality in Klebsiella pneumoniae bacteremia: a systematic review and meta-analysis","volume":"38","author":"PP Kohler","year":"2017","journal-title":"infection control & hospital epidemiology"},{"issue":"1","key":"pone.0292288.ref007","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1093\/infdis\/jix524","article-title":"An analysis of the epidemic of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae: convergence of two evolutionary mechanisms creates the \u201cperfect 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Biology"},{"issue":"1","key":"pone.0292288.ref013","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1080\/21505594.2021.1924019","article-title":"Genetic diversity and evolution of the virulence plasmids encoding aerobactin and salmochelin in Klebsiella pneumoniae","volume":"12","author":"D Tian","year":"2021","journal-title":"Virulence"},{"key":"pone.0292288.ref014","doi-asserted-by":"crossref","first-page":"182","DOI":"10.3389\/fcimb.2017.00182","article-title":"Outbreak by hypermucoviscous Klebsiella pneumoniae ST11 isolates with carbapenem resistance in a tertiary hospital in China.","volume":"7","author":"L Zhan","year":"2017","journal-title":"Frontiers in cellular and infection microbiology"},{"key":"pone.0292288.ref015","doi-asserted-by":"crossref","first-page":"149859","DOI":"10.1016\/j.scitotenv.2021.149859","article-title":"Global surveillance of antimicrobial resistance and hypervirulence in Klebsiella pneumoniae from LMICs: an in-silico approach","volume":"802","author":"R Silvester","year":"2022","journal-title":"Science of the Total Environment"},{"issue":"1","key":"pone.0292288.ref016","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s12941-022-00514-6","article-title":"Comparative in silico characterization of Klebsiella pneumoniae hypervirulent plasmids and their antimicrobial resistance genes","volume":"21","author":"N Bolourchi","year":"2022","journal-title":"Annals of Clinical Microbiology and Antimicrobials"},{"key":"pone.0292288.ref017","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.jgar.2023.01.013","article-title":"A novel transposon Tn7540 carrying blaNDM-9 and fosA3 in chromosome of a pathogenic multidrug-resistant Salmonella enterica serovar Indiana isolated from human faeces","volume":"33","author":"Y Sun","year":"2023","journal-title":"Journal of Global Antimicrobial Resistance"},{"key":"pone.0292288.ref018","first-page":"1","article-title":"ClustAGE: a tool for 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Therapy"},{"key":"pone.0292288.ref024","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/j.jgar.2022.01.016","article-title":"Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: human and non-human settings may share high-risk clones","volume":"28","author":"EI Campos-Madueno","year":"2022","journal-title":"Journal of global antimicrobial resistance"},{"key":"pone.0292288.ref025","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1016\/j.jgar.2020.03.023","article-title":"Genomic characteristics of clinically important ST11 Klebsiella pneumoniae strains worldwide","volume":"22","author":"J Zhao","year":"2020","journal-title":"Journal of Global Antimicrobial Resistance"},{"issue":"12","key":"pone.0292288.ref026","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.3390\/pathogens11121394","article-title":"A Comprehensive Genomic Analysis of the Emergent Klebsiella pneumoniae ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain","volume":"11","author":"RO de Sales","year":"2022","journal-title":"Pathogens"},{"issue":"2","key":"pone.0292288.ref027","doi-asserted-by":"crossref","first-page":"234","DOI":"10.3390\/antibiotics12020234","article-title":"Carbapenem-resistant Klebsiella pneumoniae: Virulence factors, molecular epidemiology and latest updates in treatment options","volume":"12","author":"T Karampatakis","year":"2023","journal-title":"Antibiotics"},{"key":"pone.0292288.ref028","doi-asserted-by":"crossref","first-page":"104429","DOI":"10.1016\/j.micpath.2020.104429","article-title":"Identification of plasmids by PCR based replicon typing in bacteremic Klebsiella pneumoniae","volume":"148","author":"C Shankar","year":"2020","journal-title":"Microbial pathogenesis"},{"issue":"5","key":"pone.0292288.ref029","doi-asserted-by":"crossref","first-page":"951","DOI":"10.3390\/microorganisms9050951","article-title":"First Report of bla NDM-1 Bearing IncX3 Plasmid in Clinically Isolated ST11 Klebsiella pneumoniae from Pakistan","volume":"9","author":"H Bilal","year":"2021","journal-title":"Microorganisms"},{"issue":"6","key":"pone.0292288.ref030","first-page":"e00917","article-title":"Dissemination and stability of the bla NDM-5-carrying IncX3-type plasmid among multiclonal Klebsiella pneumoniae isolates","volume":"5","author":"W Zhu","year":"2020","journal-title":"Msphere"},{"issue":"1","key":"pone.0292288.ref031","doi-asserted-by":"crossref","first-page":"6155","DOI":"10.1038\/s41467-022-33871-z","article-title":"Structural insight into Tn3 family transposition mechanism","volume":"13","author":"AV Shkumatov","year":"2022","journal-title":"Nature communications"},{"key":"pone.0292288.ref032","doi-asserted-by":"crossref","first-page":"2901","DOI":"10.2147\/IDR.S253631","article-title":"Prevalence and distribution characteristics of blaKPC-2 and blaNDM-1 genes in Klebsiella pneumoniae","author":"X Zhang","year":"2020","journal-title":"Infection and 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Can","year":"2018","journal-title":"Journal of Antimicrobial Chemotherapy"},{"issue":"3","key":"pone.0292288.ref036","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.cmi.2018.11.004","article-title":"Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232","volume":"25","author":"P Espinal","year":"2019","journal-title":"Clinical Microbiology and Infection"},{"key":"pone.0292288.ref037","author":"S Shukla","year":"2023","journal-title":"Diversity and Distribution of \u03b2-lactamase Genes Circulating in Indian Isolates of Multi-drug Resistant Klebsiella pneumoniae"},{"key":"pone.0292288.ref038","first-page":"1","article-title":"Transferable IncX3 plasmid harboring bla NDM-1, ble MBL, and aph (3\u2019)-VI genes from Klebsiella pneumoniae conferring phenotypic carbapenem resistance in E. coli","author":"AA Elshamy","year":"2023","journal-title":"Molecular Biology Reports"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0292288","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,16]],"date-time":"2023-11-16T13:30:37Z","timestamp":1700141437000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0292288"}},"subtitle":[],"editor":[{"given":"Farah","family":"Al-Marzooq","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,11,16]]},"references-count":38,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2023,11,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0292288","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,16]]}}}