{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T02:42:17Z","timestamp":1790044937849,"version":"4.0.1"},"reference-count":49,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2022,10,26]],"date-time":"2022-10-26T00:00:00Z","timestamp":1666742400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Fribourg, Switzerland"},{"name":"National Reference Center for Emerging Antibiotic Resistance (NARA)"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>An extensively drug-resistant Escherichia coli clinical isolate (N1606) belonging to Sequence Type 361 was recovered from the urine of a patient hospitalized in Switzerland. The strain showed resistance to virtually all \u03b2-lactams including the latest generation antibiotics cefiderocol and aztreonam\u2013avibactam. Whole genome sequencing revealed that it possessed two carbapenemase-encoding genes, namely blaNDM-5 and blaKPC-3, and a series of additional \u03b2-lactamase genes, including blaCTX-M-15 and blaSHV-11 encoding extended-spectrum \u03b2-lactamases (ESBLs), blaCMY-145 encoding an AmpC-type cephalosporinase, and blaOXA-1 encoding a narrow-spectrum class D \u00df-lactamase. Most of these resistance genes were located on plasmids (IncFII-FIA, IncX3, IncI\u03b3, IncFII). That strain exhibited also a four amino-acid insertion in its penicillin-binding protein 3 (PBP3) sequence, namely corresponding to YRIN. Complete genome analysis revealed that this E. coli isolate carried virulence factors (sitA, gad, hra, terC, traT, and cia) and many other non-\u03b2-lactam resistance determinants including rmtB, tet(A), dfrA17 (two copies), aadA1, aadA5 (two copies), sul1 (two copies), qacE (two copies), qepA, mdf(A), catA1, erm(B), mph(A), and qnrS1, being susceptible only to tigecycline, colistin and fosfomycin. In conclusion, we described here the phenotypic and genome characteristics of an extensively drug-resistant (XDR) E. coli ST361 being recognized as an emerging clone worldwide.<\/jats:p>","DOI":"10.3390\/antibiotics11111479","type":"journal-article","created":{"date-parts":[[2022,10,26]],"date-time":"2022-10-26T07:17:48Z","timestamp":1666768668000},"page":"1479","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Genomic Characterization of an Extensively Drug-Resistant Extra-Intestinal Pathogenic (ExPEC) Escherichia coli Clinical Isolate Co-Producing Two Carbapenemases and a 16S rRNA Methylase"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3983-3862","authenticated-orcid":false,"given":"Mustafa","family":"Sadek","sequence":"first","affiliation":[{"name":"Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland"},{"name":"Department of Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena 83522, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alaaeldin Mohamed","family":"Saad","sequence":"additional","affiliation":[{"name":"Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland"},{"name":"Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrice","family":"Nordmann","sequence":"additional","affiliation":[{"name":"Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland"},{"name":"INSERM European Unit (IAME), University of Fribourg, 1700 Fribourg, Switzerland"},{"name":"Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, 1700 Fribourg, Switzerland"},{"name":"Institute for Microbiology, Lausanne University Hospital and University of Lausanne, 1015 Lausanne, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5160-5286","authenticated-orcid":false,"given":"Laurent","family":"Poirel","sequence":"additional","affiliation":[{"name":"Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland"},{"name":"INSERM European Unit (IAME), University of Fribourg, 1700 Fribourg, Switzerland"},{"name":"Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, 1700 Fribourg, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,10,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e0066422","DOI":"10.1128\/aem.00664-22","article-title":"The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 Years in France","volume":"88","author":"Marin","year":"2022","journal-title":"Appl. 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