{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T16:02:46Z","timestamp":1790352166533,"version":"4.1.0"},"reference-count":25,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T00:00:00Z","timestamp":1762300800000},"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":"\n Background<\/jats:title>\n \n Raoultella ornithinolytica<\/jats:italic>\n is an infrequent opportunistic pathogen capable of causing multi-site infections and frequently harboring a broad array of resistance determinants, thereby complicating antimicrobial therapy. Here we report the genomic characterization of the extensively drug-resistant strain FAHZZU6693, which concurrently harbors\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n ,\n bla<\/jats:italic>\n KPC-2<\/jats:sub>\n ,\n mcr-10<\/jats:italic>\n genes and\n tmexCD2-toprJ2<\/jats:italic>\n resistance cluster.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n Matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and average nucleotide identity (ANI) were employed to confirm the species identity as\n R. ornithinolytica<\/jats:italic>\n . Antimicrobial susceptibility testing (AST) delineated the corresponding antimicrobial phenotypes. S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blotting and whole-genome sequencing (WGS) elucidated the isolate\u2019s complete molecular architecture.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Globally,\n R. ornithinolytica<\/jats:italic>\n strains harboring related resistance genes exhibit diverse geographical distribution. Strain FAHZZU6693 is resistant to most antibiotics, except amikacin and chloramphenicol. The\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n ,\n bla<\/jats:italic>\n KPC-2<\/jats:sub>\n ,\n mcr-10<\/jats:italic>\n genes and the\n tmexCD2-toprJ2<\/jats:italic>\n cluster in this strain are plasmid-borne. These occur in conserved genetic contexts:\n xerC-mcr-10-<\/jats:italic>\n IS\n Ec36-<\/jats:italic>\n IS\n Ec27-<\/jats:italic>\n IS\n Ecl1<\/jats:italic>\n and\n umuC-<\/jats:italic>\n IS\n 881-tmexC2-tmexD2-toprJ2-umuC<\/jats:italic>\n . Further analysis indicates that the insertion sequence IS\n Ec27<\/jats:italic>\n and the gene element\n umuC<\/jats:italic>\n play a crucial role in the dissemination of the\n mcr-10<\/jats:italic>\n gene and the\n tmexCD2-toprJ2<\/jats:italic>\n gene cluster.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n \n This study combines database analysis to comprehensively describe the distribution of\n R. ornithinolytica<\/jats:italic>\n strains carrying the target genes and characterizes the genomic features of a clinically Multi-drug resistant strain, providing a theoretical foundation for preventing the spread of such bacteria.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fcimb.2025.1675929","type":"journal-article","created":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T06:27:27Z","timestamp":1762324047000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["The emergence and spread of blaNDM-1, blaKPC-2, mcr-10 genes, and the tmexCD2-toprJ2 gene cluster in extensively drug-resistant clinical Raoultella ornithinolytica"],"prefix":"10.3389","volume":"15","author":[{"given":"Yafei","family":"Ye","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuting","family":"Rao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haowei","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruyan","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenyu","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanhao","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaobing","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,11,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1502528","article-title":"Dissemination of clinical Escherichia coli harboring the mcr-1 gene in Pakistan","volume":"15","author":"Abdullah","year":"2024","journal-title":"Front. Microbiol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"3240","DOI":"10.1038\/s41564-024-01844-1","article-title":"Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids","volume":"9","author":"Ares-Arroyo","year":"2024","journal-title":"Nat. Microbiol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"e02156","DOI":"10.1016\/j.idcr.2025.e02156","article-title":"Fatal case of sepsis caused by Raoultella ornithinolytica: A rare opportunistic pathogen","volume":"39","author":"Assadi","year":"2025","journal-title":"IDCases."},{"key":"B4","doi-asserted-by":"publisher","first-page":"4129","DOI":"10.1128\/JCM.01502-09","article-title":"First descriptions of blaKPC in Raoultella spp. (R. planticola and R. ornithinolytica): report from the SENTRY Antimicrobial Surveillance Program","volume":"47","author":"Castanheira","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1843","DOI":"10.1080\/22221751.2020.1803769","article-title":"Identification of novel tetracycline resistance gene tet(X14) and its co-occurrence with tet(X2) in a tigecycline-resistant and colistin-resistant Empedobacter stercoris","volume":"9","author":"Cheng","year":"2020","journal-title":"Emerg. Microbes Infect."},{"key":"B6","doi-asserted-by":"publisher","first-page":"2360","DOI":"10.1038\/s41598-020-59341-4","article-title":"Coexistence of the blaNDM-1-carrying plasmid pWLK-NDM and the blaKPC-2-carrying plasmid pWLK-KPC in a Raoultella ornithinolytica isolate","volume":"10","author":"Dang","year":"2020","journal-title":"Sci. Rep."},{"key":"B7","doi-asserted-by":"publisher","first-page":"004758","DOI":"10.12890\/2024_004758","article-title":"A case of raoultella ornithinolytica cholangitis in A liver transplant recipient","volume":"11","author":"De Coster","year":"2024","journal-title":"Eur. J. Case Rep. Intern. Med."},{"key":"B8","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1016\/j.jiac.2023.01.023","article-title":"Clinical characteristics of Raoultella ornithinolytica bacteremia and antimicrobial susceptibility of Raoultella ornithinolytica","volume":"29","author":"Etani","year":"2023","journal-title":"J. Infect. Chemother."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1097\/ICB.0000000000001758","article-title":"First report of Raoultella ornithinolytica endophthalmitis","author":"Giran","year":"2025","journal-title":"Retin Cases Brief Rep"},{"key":"B10","doi-asserted-by":"publisher","first-page":"e0021321","DOI":"10.1128\/JCM.00213-21","article-title":"Overview of changes to the clinical and laboratory standards institute performance standards for antimicrobial susceptibility testing, M100, 31st edition","volume":"59","author":"Humphries","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"e64742","DOI":"10.7759\/cureus.64742","article-title":"Raoultella ornithinolytica urinary tract infection in a patient with triple-negative breast cancer","volume":"16","author":"Jones","year":"2024","journal-title":"Cureus."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1092","DOI":"10.1128\/AAC.02147-12","article-title":"First report of blaNDM-1 in Raoultella ornithinolytica","volume":"57","author":"Khajuria","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"B13","doi-asserted-by":"publisher","first-page":"128049","DOI":"10.1016\/j.micres.2025.128049","article-title":"Rapid emergence, transmission, and evolution of KPC and NDM coproducing carbapenem-resistant Klebsiella pneumoniae","volume":"293","author":"Li","year":"2025","journal-title":"Microbiol. Res."},{"key":"B14","doi-asserted-by":"publisher","first-page":"101139","DOI":"10.1016\/j.drup.2024.101139","article-title":"Fusion event mediated by IS903B between chromosome and plasmid in two MCR-9- and KPC-2-co-producing Klebsiella pneumoniae isolates","volume":"77","author":"Liu","year":"2024","journal-title":"Drug Resist. Updat."},{"key":"B15","first-page":"7","article-title":"Acute encephalopathy in a patient with raoultella ornithinolytica infection: A challenging presentation","volume":"107","author":"Mader","year":"2013","journal-title":"R I Med. J."},{"key":"B16","doi-asserted-by":"publisher","first-page":"266","DOI":"10.3390\/antibiotics8040266","article-title":"The Inc FII Plasmid and its Contribution in the Transmission of blaNDM-1 and blaKPC-2 in Klebsiella pneumoniae in Egypt","volume":"8","author":"Mohamed","year":"2019","journal-title":"Antibiotics (Basel)."},{"key":"B17","doi-asserted-by":"publisher","first-page":"4773","DOI":"10.1021\/acs.biochem.7b00560","article-title":"Identification of the dimer exchange interface of the bacterial DNA damage response protein umud","volume":"56","author":"Murison","year":"2017","journal-title":"Biochemistry."},{"key":"B18","doi-asserted-by":"publisher","first-page":"e00088","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":"B19","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00458","article-title":"Production of plasmid-encoding NDM-1 in clinical Raoultella ornithinolytica and Leclercia adecarboxylata from China","volume":"6","author":"Sun","year":"2015","journal-title":"Front. Microbiol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"e02229","DOI":"10.1128\/AAC.02229-20","article-title":"A Novel Transferable Resistance-Nodulation-Division Pump Gene Cluster, tmexCD2-toprJ2, Confers Tigecycline Resistance in Raoultella ornithinolytica","volume":"65","author":"Wang","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00228","article-title":"Emergence of Colistin Resistance Gene mcr-8 and Its Variant in Raoultella ornithinolytica","volume":"10","author":"Wang","year":"2019","journal-title":"Front. Microbiol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"W587","DOI":"10.1093\/nar\/gkad359","article-title":"Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees","volume":"51","author":"Xie","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B23","doi-asserted-by":"crossref","first-page":"800938","DOI":"10.3389\/fmicb.2021.800938","article-title":"Nosocomial Outbreak of Carbapenemase-Producing Proteus mirabilis With Two Novel Salmonella Genomic Island 1 Variants Carrying Different blaNDM-1 Gene Copies in China","volume":"12","author":"Yang","year":"2021","journal-title":"Front. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"167373","DOI":"10.1016\/j.scitotenv.2023.167373","article-title":"Conjugative plasmids facilitate the transmission of tmexCD2-toprJ2 among carbapenem-resistant Klebsiella pneumoniae","volume":"906","author":"Yao","year":"2024","journal-title":"Sci. Total Environ."},{"key":"B25","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1016\/j.jgar.2025.01.021","article-title":"The co-occurrence of tet(X4) and tmexCD2-toprJ2 mediated tigecycline resistance in Raoultella ornithinolytica","volume":"42","author":"Zhai","year":"2025","journal-title":"J. Glob Antimicrob. Resist."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1675929\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T06:27:28Z","timestamp":1762324048000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1675929\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,5]]},"references-count":25,"alternative-id":["10.3389\/fcimb.2025.1675929"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2025.1675929","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,5]]},"article-number":"1675929"}}