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Government","award":["PI17\/01405"],"award-info":[{"award-number":["PI17\/01405"]}]},{"name":"Agencia Estatal de Investigaci\u00f3n\/Ministry of Science and Innovation of the Spanish Government","award":["PI20\/01255"],"award-info":[{"award-number":["PI20\/01255"]}]},{"name":"Agencia Estatal de Investigaci\u00f3n\/Ministry of Science and Innovation of the Spanish Government","award":["US-1381501"],"award-info":[{"award-number":["US-1381501"]}]},{"name":"Agencia Estatal de Investigaci\u00f3n\/Ministry of Science and Innovation of the Spanish Government","award":["PID2023-150077OB-I00\/AEI\/10.13039\/501100011033\/FEDER"],"award-info":[{"award-number":["PID2023-150077OB-I00\/AEI\/10.13039\/501100011033\/FEDER"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Background: Urinary tract infections are a global health concern, with uropathogenic Escherichia coli (UPEC) accounting for 80\u201390% of cases. Given the rise in antimicrobial resistance, our aim was to elucidate the genetic mechanisms behind low-level resistance to ciprofloxacin and fosfomycin (LLCR and LLFR) in UPEC strains, using whole-genome sequencing (WGS) to identify point mutations in chromosomal and plasmid genes. Methods: A cohort UPEC was collected from kidney transplant recipients at the Virgen del Roc\u00edo University Hospital, Spain. Minimum inhibitory concentrations were determined for ciprofloxacin and fosfomycin to categorize strains into LLCR and LLFR. Twenty strains were selected for WGS, with genome annotations. Point mutations were identified and analyzed using alignment tools, and protein stability changes were predicted. Results: LLCR strains exhibited mutations in key quinolone resistance-determining regions of the gyrA gene, in 83% of cases. The qnrS1 plasmid gene was found in 17% of LLCR strains. LLFR strains showed mutations in the glpT and cyaA genes. Mutations in the uhp gene family were linked to the fosfomycin-resistant phenotype, suggesting a multi-step resistance evolution mechanism. Conclusions: This study highlights the complex interplay between chromosomal and plasmid genes in UPEC\u2019s resistance to ciprofloxacin and fosfomycin. The findings contribute to understanding low-level resistance mechanisms and may guide the development of novel therapeutic strategies to combat multidrug-resistant strains.<\/jats:p>","DOI":"10.3390\/biom15020260","type":"journal-article","created":{"date-parts":[[2025,2,11]],"date-time":"2025-02-11T10:53:22Z","timestamp":1739271202000},"page":"260","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Detection of Possible Resistance Mechanisms in Uropathogenic Escherichia coli Strains Isolated from Kidney Transplant Recipients Based on Whole Genome Sequencing"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8019-0905","authenticated-orcid":false,"given":"Soraya","family":"Herrera-Espejo","sequence":"first","affiliation":[{"name":"Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital\/CSIC\/University of Seville, 41013 Seville, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6736-6141","authenticated-orcid":false,"given":"Alejandro","family":"Rubio","sequence":"additional","affiliation":[{"name":"Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA), Faculty of Experimental Sciences (Genetics Area), University Pablo de Olavide, 41013 Seville, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luc\u00eda","family":"Ceballos-Romero","sequence":"additional","affiliation":[{"name":"Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital\/CSIC\/University of Seville, 41013 Seville, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8166-5308","authenticated-orcid":false,"given":"Jer\u00f3nimo","family":"Pach\u00f3n","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital\/CSIC\/University of Seville, 41013 Seville, Spain"},{"name":"Department of Medicine, School of Medicine, University of Seville, 41004 Seville, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7766-7266","authenticated-orcid":false,"given":"Elisa","family":"Cordero","sequence":"additional","affiliation":[{"name":"Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital\/CSIC\/University of Seville, 41013 Seville, Spain"},{"name":"Department of Medicine, School of Medicine, University of Seville, 41004 Seville, Spain"},{"name":"CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3343-2822","authenticated-orcid":false,"given":"Antonio J.","family":"P\u00e9rez-Pulido","sequence":"additional","affiliation":[{"name":"Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA), Faculty of Experimental Sciences (Genetics Area), University Pablo de Olavide, 41013 Seville, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7969-8162","authenticated-orcid":false,"given":"Mar\u00eda Eugenia","family":"Pach\u00f3n-Ib\u00e1\u00f1ez","sequence":"additional","affiliation":[{"name":"Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital\/CSIC\/University of Seville, 41013 Seville, Spain"},{"name":"CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/nrmicro3432","article-title":"Urinary tract infections: Epidemiology, mechanisms of infection and treatment options","volume":"13","author":"Walker","year":"2015","journal-title":"Nat. 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