{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T21:50:20Z","timestamp":1785793820389,"version":"3.56.0"},"reference-count":33,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T00:00:00Z","timestamp":1762473600000},"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 Carbapenem-resistant Enterobacter cloacae complex (ECC) has emerged as the third most prevalent nosocomial Enterobacterales pathogen, propelled by the synergy between intrinsic defenses, e.g. AcrAB-TolC efflux pump overexpression and horizontally acquired determinants such as the plasmid-borne\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n .\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n Our study employed a comprehensive, multi-faceted strategy to characterize three carbapenem-resistant, NDM-1-positive ECC isolates, named x9, F12, and x230151. The integrated methodology merged phenotypic antimicrobial susceptibility testing with functional conjugation and electroporation assays. High-resolution hybrid Nanopore-Illumina genome assemblies enabled detailed genomic annotation and extensive resistance profiling. We further quantified\n acrAB-tolC<\/jats:italic>\n efflux pump expression via quantitative RT-PCR and reconstructed the evolutionary history of the\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n -\n ble<\/jats:italic>\n MBL<\/jats:sub>\n module using comparative plasmid genomics.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n All three ECC isolates were extensively Drug-Resistant (XDR) with carbapenem MICs \u2265 8 mg\/L. Genomes carried 33\u201335 resistance loci, including &gt; 5-fold up-regulated\n acrAB-tolC<\/jats:italic>\n on chromosome, and constitutive chromosomal expression of\n bla<\/jats:italic>\n ACT<\/jats:sub>\n -type AmpC further blunted the activity of cephalosporins and carbapenems. The\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n -\n ble<\/jats:italic>\n MBL<\/jats:sub>\n resided on ~110\u2013240 kb IncF\/IncN\/IncX3 plasmids that transferred at 3-8\u00d710\u2013\n 3<\/jats:sup>\n per donor and were embedded in Tn\n 125<\/jats:italic>\n \/Tn\n 3000<\/jats:italic>\n transposons flanked by IS\n Aba125<\/jats:italic>\n \/IS\n 26<\/jats:italic>\n . These replicons also carried ESBLs (\n bla<\/jats:italic>\n CTX-M-15<\/jats:sub>\n ),\n bla<\/jats:italic>\n TEM-1<\/jats:sub>\n , aminoglycoside- modifying enzymes (\n armA<\/jats:italic>\n ,\n aadA1<\/jats:italic>\n ) and intact class 1 integrons (In2, In799 and In1465). Despite&gt;90% backbone identity of the\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n -\n ble<\/jats:italic>\n MBL<\/jats:sub>\n , the module could be reversibly excised, inverted or truncated, allowing rapid \u201cgene-offload\u201d and re-acquisition under shifting antibiotic pressure.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n Once the carbapenem MIC surpassed 8 mg\/L, the tandem action of the chromosomally over-expressed AcrAB-TolC efflux pump and plasmid-borne\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n carbapenemase rendered ECC virtually untreatable. Mutations in\n ramR<\/jats:italic>\n and\n soxR<\/jats:italic>\n regulators, as well as promoter insertions or deletions that amplify either system should also be tracked in real-time via sustained surveillance.Effective containment would require combination strategies that simultaneously inhibit efflux, neutralize \u03b2-lactamase activity, and destabilized or eliminated the IncF\/IncN\/IncX3 plasmids carrying\n bla<\/jats:italic>\n NDM-1<\/jats:sub>\n .\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fcimb.2025.1705370","type":"journal-article","created":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T11:03:15Z","timestamp":1762513395000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Characterization of Enterobacter cloacae complex clinical isolates: comparative genomics and the role of the efflux pump AcrAB-TolC over-expression and NDM-1 production"],"prefix":"10.3389","volume":"15","author":[{"given":"Nan","family":"Jiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faxiao","family":"Pu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenji","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongguo","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayu","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,11,7]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.1038\/s41467-022-28819-2","article-title":"Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM","volume":"13","author":"Acman","year":"2022","journal-title":"Nat. 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