{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T05:54:09Z","timestamp":1791179649561,"version":"4.1.0"},"reference-count":72,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000},"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. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>\n                      Multiple-carbapenemase-producing\n                      <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                      has emerged as a critical threat to global health due to limited treatment options and high mortality. This study aimed to characterize the genomic features of a triple-carbapenemase-producing\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      clinical isolate.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      A carbapenem-resistant\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      (CRKP) strain K27 was collected from a patient in a tertiary hospital in January 2025. Antimicrobial susceptibility testing, carbapenemase detection, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), conjugation experiments, and plasmid fitness cost assays were performed. Whole-genome sequencing (WGS) of strain K27 was carried out on Illumina and PacBio platforms, bioinformatic analyses were performed using tools such as PlasmidFinder, ResFinder and ISfinder to characterize plasmid architecture, including replicon typing, resistance gene profiling, and mobile genetic element identification.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Strain K27 was an extensively drug-resistant ST11\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      producing three carbapenemases (NDM, KPC and VIM). Both S1-PFGE and WGS revealed that strain K27 carried four plasmids. The\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>KPC-2<\/jats:sub>\n                      gene was located on an IncFII\n                      <jats:sub>pHN7A8<\/jats:sub>\n                      :IncR hybrid plasmid (assigned as pK27-KPC2) and carried by a truncated transposon Tn\n                      <jats:italic>6296<\/jats:italic>\n                      , while the\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>NDM-5<\/jats:sub>\n                      and\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>VIM-1<\/jats:sub>\n                      genes were co-harboured on a single IncA plasmid (assigned as pK27-NDM5\/VIM1), where they were carried by a truncated transposon Tn\n                      <jats:italic>125<\/jats:italic>\n                      and integron In916, respectively. The two corresponding genetic elements were separated by IS\n                      <jats:italic>CR1<\/jats:italic>\n                      , and this arrangement was highly similar to that of plasmid p24A20009_B_NDM. Conjugation experiments demonstrated that the plasmid pK27-NDM5\/VIM1 was transferable at a frequency of (4.5\u202f\u00b1\u202f1.2)\u202f\u00d7\u202f10\n                      <jats:sup>\u22122<\/jats:sup>\n                      , and the resulting transconjugant was designated as K27-C. Independent sample\n                      <jats:italic>t<\/jats:italic>\n                      -tests further revealed significant differences between the transconjugant K27-C and the\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      J53Azi\n                      <jats:sup>R<\/jats:sup>\n                      groups, both in the area under the curve (\n                      <jats:italic>t<\/jats:italic>\n                      =\u202f3.63,\n                      <jats:italic>p<\/jats:italic>\n                      =\u202f0.002) and in the maximum optical density (\n                      <jats:italic>t<\/jats:italic>\n                      =\u202f2.57,\n                      <jats:italic>p<\/jats:italic>\n                      =\u202f0.02).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      The finding of two different class B metallo-carbapenemase genes co-harboured on a single conjugative IncA plasmid in a KPC-producing ST11\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      clinical isolate is alarming. This co-production of three distinct carbapenemases in a single strain could pose considerable challenges for the selection of clinical anti-infective therapies. Furthermore, the isolate may pose a high risk of subsequent clonal dissemination and\/or horizontal gene transfer, necessitating ongoing epidemiological surveillance.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1959757","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T05:32:57Z","timestamp":1791178377000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Characterization of a conjugative IncA plasmid co-harbouring blaNDM-5 and blaVIM-1 in a KPC-producing Klebsiella pneumoniae clinical isolate K27"],"prefix":"10.3389","volume":"17","author":[{"given":"Zhenzhen","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dandan","family":"Dong","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nan","family":"Jia","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youhan","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Clinical Chemistry and Laboratory Medicine, Hietzing Hospital, Vienna Healthcare Group","place":["Vienna, Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanqi","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University","place":["Qingdao, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,10,5]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"228","DOI":"10.3855\/jidc.10969","article-title":"Co-existence of blandm-1 and blaVIM-1 producing Moellerella wisconsensis in Nicu of north Indian hospital","volume":"14","author":"Ahmad","year":"2020","journal-title":"J. Infect. Dev. Ctries."},{"key":"ref2","doi-asserted-by":"publisher","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":"Alonso-del Valle","year":"2021","journal-title":"Nat. Commun."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.plasmid.2018.02.002","article-title":"Compatibility and entry exclusion of IncA and IncC plasmids revisited: IncA and IncC plasmids are compatible","author":"Ambrose","year":"2018","journal-title":"Plasmid"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"7957","DOI":"10.1021\/acs.chemrev.1c00138","article-title":"Metallo-\u03b2-lactamases in the age of multidrug resistance: from structure and mechanism to evolution, dissemination, and inhibitor design","volume":"121","author":"Bahr","year":"2021","journal-title":"Chem. Rev."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"1681413","DOI":"10.3389\/fmicb.2025.1681413","article-title":"Correction: Integrons in the development of antimicrobial resistance: critical review and perspectives","volume":"16","author":"Bhat","year":"2025","journal-title":"Front. Microbiol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"W29","DOI":"10.1093\/nar\/gkt282","article-title":"BLAST: a more efficient report with usability improvements","volume":"41","author":"Boratyn","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"294","DOI":"10.3389\/fmicb.2015.00294","article-title":"NDM-1 encoded by a pNDM-BJ01-like plasmid p3sP-NDM in clinical Enterobacter aerogenes","volume":"6","author":"Chen","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref9001","article-title":"Methods for antimicrobial dilution and disk susceptibility testing of infrequently isolated or fastidious bacteria","year":"2015"},{"key":"ref9002","article-title":"Performance Standards for Antimicrobial Susceptibility Testing","year":"2026"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/s41586-021-04233-4","article-title":"Towards the biogeography of prokaryotic genes","volume":"601","author":"Coelho","year":"2022","journal-title":"Nature"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"4207","DOI":"10.1128\/AAC.02773-13","article-title":"Complete nucleotide sequence of two multidrug-resistant IncR plasmids from Klebsiella pneumoniae","volume":"58","author":"Compain","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1089\/mdr.2021.0466","article-title":"Emergence of urease-negative Klebsiella pneumoniae St340 carrying an IncP6 plasmid-mediated bla(KPC-2) gene","volume":"28","author":"Di Conza","year":"2022","journal-title":"Microb. Drug Resist."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"2030","DOI":"10.3389\/fmicb.2019.02030","article-title":"Characterization of a NDM-1-encoding plasmid pHFK418-NDM from a clinical Proteus mirabilis isolate Harboring two novel transposons, Tn6624 and Tn6625","volume":"10","author":"Dong","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/s12866-025-04575-3","article-title":"Colonization with Carbapenemase producing Enterobacterales (CPE) and associated alteration in microbiota composition in a tertiary care hospital in Egypt","volume":"26","author":"El-Defrawy","year":"2026","journal-title":"BMC Microbiol."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"26723","DOI":"10.1038\/s41598-024-78205-9","article-title":"The characterization of an IncN\u2013IncR fusion plasmid co-harboring bla(TEM-40), bla(KPC-2), and bla(IMP-4) derived from St1393 Klebsiella pneumoniae","volume":"14","author":"Fang","year":"2024","journal-title":"Sci. Rep."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"4750","DOI":"10.1128\/JB.00189-09","article-title":"Comparative genomics of the IncA\/C multidrug resistance plasmid family","volume":"191","author":"Fricke","year":"2009","journal-title":"J. Bacteriol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/j.ijantimicag.2019.03.014","article-title":"Pandemic spread of bla((KPC-2)) among Klebsiella pneumoniae St11 in China is associated with horizontal transfer mediated by IncFII-like plasmids","volume":"54","author":"Fu","year":"2019","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.3390\/antibiotics11081108","article-title":"Characterization of carbapenem-resistant K. pneumoniae isolated from intensive care units of Zagazig University hospitals","volume":"11","author":"Gandor","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"186","DOI":"10.3390\/antibiotics9040186","article-title":"The current burden of carbapenemases: review of significant properties and dissemination among gram-negative bacteria","volume":"9","author":"Hammoudi Halat","year":"2020","journal-title":"Antibiotics (Basel)"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"e00762","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":"ref21","doi-asserted-by":"publisher","first-page":"5952","DOI":"10.1128\/AAC.05108-11","article-title":"A novel variant, NDM-5, of the New Delhi metallo-\u03b2-lactamase in a multidrug-resistant Escherichia coli St648 isolate recovered from a patient in the United Kingdom","volume":"55","author":"Hornsey","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"4188","DOI":"10.1038\/s41467-021-24448-3","article-title":"A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex","volume":"12","author":"Lam","year":"2021","journal-title":"Nat. Commun."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"1584","DOI":"10.1128\/AAC.43.7.1584","article-title":"Cloning and characterization of blavim, a new integron-borne metallo-beta-lactamase gene from a Pseudomonas aeruginosa clinical isolate","volume":"43","author":"Lauretti","year":"1999","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"2472","DOI":"10.3389\/fmicb.2019.02472","article-title":"Complex class 1 integron in a clinical Escherichia coli strain from Vietnam carrying both mcr-1 and Bla (NDM-1)","volume":"10","author":"Le-Vo","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"14418","DOI":"10.1038\/s41598-024-65106-0","article-title":"Distribution and molecular characterization of carbapenemase-producing gram-negative bacteria in Henan, China","volume":"14","author":"Li","year":"2024","journal-title":"Sci. Rep."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"106222","DOI":"10.1016\/j.ebiom.2026.106222","article-title":"Clinical characteristics and molecular epidemiology of kpc-Ndm co-producing carbapenem-resistant Klebsiella pneumoniae in China: a multicentre retrospective case-control study","volume":"126","author":"Li","year":"2026","journal-title":"EBioMedicine"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"851","DOI":"10.3201\/eid3206.260478","article-title":"Emergence of Klebsiella pneumoniae Carbapenemase-producing K. pneumoniae with penicillin-binding protein 3 insertions, Taiwan, 2021","volume":"32","author":"Long","year":"2026","journal-title":"Emerg. Infect. Dis."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","article-title":"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance","volume":"18","author":"Magiorakos","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"2249","DOI":"10.1093\/jac\/dkx148","article-title":"Genomic epidemiology of global VIM-producing Enterobacteriaceae","volume":"72","author":"Matsumura","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"1519827","DOI":"10.3389\/fcimb.2025.1519827","article-title":"Polyclonal carbapenemase-producing Escherichia coli in northern Italy: the emergence of NDM-7","volume":"15","author":"Mattioni Marchetti","year":"2025","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"6220","DOI":"10.1038\/s41598-024-55884-y","article-title":"Enterobacter asburiae St229: an emerging carbapenemases producer","volume":"14","author":"Mattioni Marchetti","year":"2024","journal-title":"Sci. Rep."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"3341","DOI":"10.3389\/fmicb.2018.03341","article-title":"Genetic diversity of carbapenem-resistant Enterobacteriaceae (CRE) clinical isolates from a tertiary hospital in eastern China","volume":"9","author":"Miao","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"dsae002","DOI":"10.1093\/dnares\/dsae002","article-title":"A comprehensive list of genes required for the efficient conjugation of plasmid Rts1 was determined by systematic deletion analysis","volume":"31","author":"Murata","year":"2024","journal-title":"DNA Res."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e0420623","DOI":"10.1128\/spectrum.04206-23","article-title":"Antibiotic resistance begets more resistance: chromosomal resistance mutations mitigate fitness costs conferred by multi-resistant clinical plasmids","volume":"12","author":"Nair","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"e0148024","DOI":"10.1128\/aem.01480-24","article-title":"Dietary zinc supplementation inhibits bacterial plasmid conjugation in vitro by regulating plasmid replication (rep) and transfer (tra) genes","volume":"90","author":"Ott","year":"2024","journal-title":"Appl. Environ. Microbiol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"e00088-17","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":"ref38","doi-asserted-by":"publisher","first-page":"116370","DOI":"10.1016\/j.diagmicrobio.2024.116370","article-title":"Carbapenemase producing gram negative bacteria: review of resistance and detection methods","volume":"110","author":"Paudel","year":"2024","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"001646","DOI":"10.1099\/mic.0.001646","article-title":"Variations in carbapenem resistance associated with the vim-1 metallo-\u03b2-lactamase across the Enterobacterales","volume":"172","author":"Rondinelli","year":"2026","journal-title":"Microbiology (Reading)"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1016\/j.tim.2018.06.007","article-title":"Evolution of plasmid-mediated antibiotic resistance in the clinical context","volume":"26","author":"San Millan","year":"2018","journal-title":"Trends Microbiol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"4333","DOI":"10.1128\/AAC.00260-09","article-title":"Novel genetic environment of the carbapenem-hydrolyzing beta-lactamase KPC-2 among Enterobacteriaceae in China","volume":"53","author":"Shen","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1186\/s12879-025-10959-7","article-title":"Prevalence of genes encoding carbapenem-resistance in Klebsiella pneumoniae recovered from clinical samples in Africa: systematic review and meta-analysis","volume":"25","author":"Sisay","year":"2025","journal-title":"BMC Infect. Dis."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"122","DOI":"10.3390\/antibiotics8030122","article-title":"Present and future of carbapenem-resistant Enterobacteriaceae (CRE) infections","volume":"8","author":"Suay-Garc\u00eda","year":"2019","journal-title":"Antibiotics (Basel)"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1007\/s12088-025-01526-4","article-title":"Molecular characterization of cariogenic, biofilm-forming, multi-drug-resistant Pseudomonas aeruginosa and detection of NDM-1 and blaVIM-1 genes","volume":"66","author":"Subramanian","year":"2026","journal-title":"Indian J. Microbiol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"e0079323","DOI":"10.1128\/spectrum.00793-23","article-title":"Evaluation of the NG-Test CARBA 5 lateral flow assay with an IMP-27-producing Morganella morganii and other Morganellaceae","volume":"11","author":"Tarlton","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e0014525","DOI":"10.1128\/mra.00145-25","article-title":"Draft genome sequence of carbapenem-resistant Klebsiella pneumoniae St6260 isolated from the catheter tip of a female patient in Nepal","volume":"14","author":"Thapa","year":"2025","journal-title":"Microbiol Resour Announc"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3201\/eid2811.220415","article-title":"Increased detection of carbapenemase-producing Enterobacterales bacteria in Latin America and the Caribbean during the Covid-19 pandemic","volume":"28","author":"Thomas","year":"2022","journal-title":"Emerg. Infect. Dis."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"5836","DOI":"10.1073\/pnas.75.12.5836","article-title":"Fertility repression of F-like conjugative plasmids: physical mapping of the R6--5 finO and finP cistrons and identification of the finO protein","volume":"75","author":"Timmis","year":"1978","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1128\/MMBR.00048-05","article-title":"ISCR elements: novel gene-capturing systems of the 21st century?","volume":"70","author":"Toleman","year":"2006","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1556\/030.2025.02559","article-title":"NDM-1 and VIM-1 dual metallo-beta-lactamase producing Klebsiella pneumoniae St15 high-risk clone from a blood culture of a patient at intensive care unit in a Greek tertiary care hospital","volume":"72","author":"Tsolakidou","year":"2025","journal-title":"Acta Microbiol. Immunol. Hung."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"D384","DOI":"10.1093\/nar\/gkac1096","article-title":"The conserved domain database in 2023","volume":"51","author":"Wang","year":"2023","journal-title":"Nucleic Acid Res."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"e0136422","DOI":"10.1128\/spectrum.01364-22","article-title":"Transmission of nonconjugative virulence or resistance plasmids mediated by a self-transferable IncN3 plasmid from carbapenem-resistant Klebsiella pneumoniae","volume":"10","author":"Wang","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"S196","DOI":"10.1093\/cid\/ciy660","article-title":"Phenotypic and genotypic characterization of carbapenem-resistant Enterobacteriaceae: data from a longitudinal large-scale CRE study in China (2012\u20132016)","volume":"67","author":"Wang","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1038\/s41396-023-01393-1","article-title":"Cooperative antibiotic resistance facilitates horizontal gene transfer","volume":"17","author":"Wang","year":"2023","journal-title":"ISME J."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"e0077621","DOI":"10.1128\/mSphere.00776-21","article-title":"Identification of a novel bla(NDM) variant, bla(NDM-33,) in an Escherichia coli isolate from hospital wastewater in China","volume":"6","author":"Wang","year":"2021","journal-title":"mSphere"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"e1005595","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":"ref58","doi-asserted-by":"publisher","first-page":"e000102","DOI":"10.1099\/mgen.0.000102","article-title":"Identification of Klebsiella capsule synthesis loci from whole genome data","volume":"2","author":"Wyres","year":"2016","journal-title":"Microb. Genom."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"105944","DOI":"10.1016\/j.ebiom.2025.105944","article-title":"Transposition of insertion sequence element from KPC plasmid enhances intracellular survival of Klebsiella pneumoniae","volume":"120","author":"Xie","year":"2025","journal-title":"EBioMedicine"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"7319","DOI":"10.1038\/s41467-025-62455-w","article-title":"Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong","volume":"16","author":"Xu","year":"2025","journal-title":"Nat. Commun."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1128\/AAC.45.4.1151-1161.2001","article-title":"Novel carbapenem-hydrolyzing beta-lactamase, kpc-1, from a carbapenem-resistant strain of Klebsiella pneumoniae","volume":"45","author":"Yigit","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"5046","DOI":"10.1128\/AAC.00774-09","article-title":"Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India","volume":"53","author":"Yong","year":"2009","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1007\/s10482-017-0844-4","article-title":"A large-scale evaluation of algorithms to calculate average nucleotide identity","volume":"110","author":"Yoon","year":"2017","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1111\/eva.13441","article-title":"Co-evolutionary adaptations of Acinetobacter baumannii and a clinical carbapenemase-encoding plasmid during carbapenem exposure","volume":"15","author":"Zhang","year":"2022","journal-title":"Evol. Appl."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"579618","DOI":"10.3389\/fmicb.2020.579618","article-title":"Co-occurrence of rapid gene gain and loss in an interhospital outbreak of carbapenem-resistant hypervirulent St11-K64 Klebsiella pneumoniae","volume":"11","author":"Zhang","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1186\/s12879-023-08242-8","article-title":"Epidemiological characteristics of New Delhi metallo-\u03b2-lactamase-producing Enterobacteriaceae in the fourth hospital of Hebei medical university","volume":"23","author":"Zhao","year":"2023","journal-title":"BMC Infect. Dis."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"922031","DOI":"10.3389\/fcimb.2022.922031","article-title":"Convergence of Mcr-8.2 and chromosome-mediated resistance to colistin and tigecycline in an NDM-5-producing St656 Klebsiella pneumoniae isolate from a lung transplant patient in China","volume":"12","author":"Zhao","year":"","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"980191","DOI":"10.3389\/fmicb.2022.980191","article-title":"Emergence of a NDM-1-producing St25 Klebsiella pneumoniae strain causing neonatal sepsis in China","volume":"13","author":"Zhao","year":"","journal-title":"Front. Microbiol."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/1471-2164-9-36","article-title":"Insertion sequences show diverse recent activities in Cyanobacteria and Archaea","volume":"9","author":"Zhou","year":"2008","journal-title":"BMC Genomics"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"115955","DOI":"10.1016\/j.diagmicrobio.2023.115955","article-title":"Risk factors and molecular epidemiology of bloodstream infections due to carbapenem-resistant Klebsiella pneumoniae","volume":"106","author":"Zhu","year":"2023","journal-title":"Diagn. Microbiol. Infect. 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