{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T20:48:10Z","timestamp":1792183690003,"version":"4.4.0"},"reference-count":65,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2024,9,13]],"date-time":"2024-09-13T00:00:00Z","timestamp":1726185600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"U.S. Food and Drug Administration","award":["E07662.01"],"award-info":[{"award-number":["E07662.01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Our whole-genome sequencing analysis of sixteen uropathogenic E. coli isolates revealed a concerning picture of multidrug resistance and potentially virulent bacteria. All isolates belonged to four distinct clonal groups, with the highly prevalent ST131 lineage being associated with extensive antibiotic resistance and virulence factors. Notably, all isolates exhibited multidrug resistance, with some resistant to as many as 12 antibiotics. Fluoroquinolone resistance stemmed primarily from efflux pumps and mutations in gyrase and topoisomerase genes. Additionally, we identified genes encoding resistance to extended-spectrum cephalosporins, trimethoprim\/sulfamethoxazole, and various heavy metals. The presence of diverse plasmids and phages suggests the potential for horizontal gene transfer and the dissemination of virulence factors. All isolates harbored genomic islands containing virulence factors associated with adhesion, biofilm formation, and invasion. Genes essential for iron acquisition, flagella biosynthesis, secretion systems, and toxin production were also prevalent. Adding further complexity to understanding the isolates\u2019 genetic makeup, we identified CRISPR-Cas systems. This study underscores the need for continued genomic surveillance in understanding the pathogenic mechanisms and resistance profiles of uropathogenic E. coli to aid in developing targeted therapeutic strategies.<\/jats:p>","DOI":"10.3390\/pathogens13090794","type":"journal-article","created":{"date-parts":[[2024,9,13]],"date-time":"2024-09-13T07:30:35Z","timestamp":1726212635000},"page":"794","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Comprehensive Genomic Analysis of Uropathogenic E. coli: Virulence Factors, Antimicrobial Resistance, and Mobile Genetic Elements"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7926-6156","authenticated-orcid":false,"given":"Kidon","family":"Sung","sequence":"first","affiliation":[{"name":"Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"Nawaz","sequence":"additional","affiliation":[{"name":"Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miseon","family":"Park","sequence":"additional","affiliation":[{"name":"Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jungwhan","family":"Chon","sequence":"additional","affiliation":[{"name":"Department of Companion Animal Health, Inje University, Gimhae 50834, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3473-8815","authenticated-orcid":false,"given":"Saeed A.","family":"Khan","sequence":"additional","affiliation":[{"name":"Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khulud","family":"Alotaibi","sequence":"additional","affiliation":[{"name":"Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashraf A.","family":"Khan","sequence":"additional","affiliation":[{"name":"Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,9,13]]},"reference":[{"key":"ref_1","first-page":"1","article-title":"Ambulatory medical care utilization estimates for 2007","volume":"169","author":"Schappert","year":"2011","journal-title":"Vital Health Stat. 13"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1093\/jac\/dkg028","article-title":"An international survey of the antimicrobial susceptibility of pathogens from uncomplicated urinary tract infections: The ECO.SENS Project","volume":"51","author":"Kahlmeter","year":"2003","journal-title":"J. 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