{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T05:11:01Z","timestamp":1793337061755,"version":"4.5.0"},"reference-count":48,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T00:00:00Z","timestamp":1715644800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004567","name":"Ministry of Education, Government of the People's Republic of Bangladesh","doi-asserted-by":"publisher","award":["LS20191223"],"award-info":[{"award-number":["LS20191223"]}],"id":[{"id":"10.13039\/501100004567","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019278","name":"Bangladesh Agricultural University Research System","doi-asserted-by":"publisher","award":["2021\/21\/BAU"],"award-info":[{"award-number":["2021\/21\/BAU"]}],"id":[{"id":"10.13039\/100019278","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Colistin resistance is a global concern warning for a one health approach to combat the challenge. Colistin resistant <jats:italic>E<\/jats:italic>. <jats:italic>coli<\/jats:italic> and their resistance determinants are widely distributed in the environment, and rats could be a potential source of these isolates and resistant determinants to a diverse environmental setting. This study was aimed to determine the presence of colistin resistant <jats:italic>E<\/jats:italic>. <jats:italic>coli<\/jats:italic> (CREC) in wild rats, their antimicrobial resistance (AMR) phenotypes, and genotypic analysis of <jats:italic>mcr-1<\/jats:italic> CREC through whole genome sequencing (WGS). A total of 39 rats were examined and CREC was isolated from their fecal pellets onto MacConkey agar containing colistin sulfate (1 \u03bcg\/ mL). AMR of the CREC was determined by disc diffusion and broth microdilution was employed to determine MIC to colistin sulfate. CREC were screened for <jats:italic>mcr<\/jats:italic> genes (<jats:italic>mcr-1<\/jats:italic> to <jats:italic>mcr-8<\/jats:italic>) and phylogenetic grouping by PCR. Finally, WGS of one <jats:italic>mcr-1<\/jats:italic> CREC was performed to explore its genetic characteristics especially resistomes and virulence determinants. 43.59% of the rats carried CREC with one (2.56%) of them carrying CREC with <jats:italic>mcr-1<\/jats:italic> gene among the <jats:italic>mcr<\/jats:italic> genes examined. Examination of seventeen (17) isolates from the CREC positive rats (n = 17) revealed that majority of them belonging to the pathogenic phylogroup D (52.94%) and B2 (11.76%). 58.82% of the CREC were MDR on disc diffusion test. Shockingly, the <jats:italic>mcr-1<\/jats:italic> CREC showed phenotypic resistance to 16 antimicrobials of 8 different classes and carried the ARGs in its genome. The <jats:italic>mcr-1<\/jats:italic> gene was located on a 60 kb IncI2 plasmid. On the other hand, ARGs related to aminoglycosides, phenicols, sulfonamides, tetracyclines and trimethoprims were located on a 288 kb mega-plasmid separately. The <jats:italic>mcr-1<\/jats:italic> CREC carried 58 virulence genes including genes related to adhesion, colonization, biofilm formation, hemolysis and immune-evasion. The isolate belonged to ST224 and closely related to <jats:italic>E<\/jats:italic>. <jats:italic>coli<\/jats:italic> from different sources including UPEC clinical isolates from human based on cgMLST analysis. The current research indicates that rats might be a possible source of CREC, and the presence of <jats:italic>mcr-1<\/jats:italic> and other ARGs on plasmid increases the risk of ARGs spreading and endangering human health and other environmental components through this infamous pest.<\/jats:p>","DOI":"10.1371\/journal.pone.0296109","type":"journal-article","created":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T17:24:07Z","timestamp":1715707447000},"page":"e0296109","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["First detection and characterization of mcr-1 colistin resistant E. coli from wild rat in Bangladesh"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1670-1448","authenticated-orcid":true,"given":"Md. 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and animal fecal samples","volume":"62","author":"RF Wang","year":"1996","journal-title":"Appl Environ Microbiol"},{"key":"pone.0296109.ref022","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES.2018.23.6.17-00672","article-title":"Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes","volume":"23","author":"AR Rebelo","year":"2018","journal-title":"Euro Surveill"},{"issue":"1","key":"pone.0296109.ref023","doi-asserted-by":"crossref","first-page":"70","DOI":"10.3390\/applmicrobiol4010005","article-title":"Occurrence of Mobile Colistin Resistance Genes mcr-1\u2013mcr-10 including Novel mcr Gene Variants in Different Pathotypes of Porcine Escherichia coli Isolates Collected in Germany from 2000 to 2021","volume":"4","author":"L G\u00f6pel","year":"2024","journal-title":"Appl 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in-depth characterization and visualization of bacterial genomes","volume":"51","author":"JR Grant","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pone.0296109.ref034","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder","volume":"76","author":"MHK Johansson","year":"2021","journal-title":"J Antimicrob Chemother"},{"key":"pone.0296109.ref035","doi-asserted-by":"crossref","DOI":"10.1098\/rsbl.2016.0137","article-title":"\u201cDisperse abroad in the land\u201d: the role of wildlife in the dissemination of antimicrobial resistance","volume":"12","author":"KE Arnold","year":"2016","journal-title":"Biol Lett"},{"key":"pone.0296109.ref036","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1292\/jvms.19-0697","article-title":"Antibiotic-resistant Escherichia coli isolated from urban rodents in Hanoi, Vietnam","volume":"82","author":"H Le Huy","year":"2020","journal-title":"J Vet Med Sci"},{"key":"pone.0296109.ref037","first-page":"17093","article-title":"Rodents on pig and chicken farms\u2014a potential threat to human and animal health","volume":"2","author":"A Backhans","year":"2012","journal-title":"Infect Ecol Epidemiol"},{"key":"pone.0296109.ref038","article-title":"Molecular Epidemiology and Colistin Resistant Mechanism of mcr-Positive and mcr-Negative Clinical Isolated Escherichia coli","volume":"8","author":"Q Luo","year":"2017","journal-title":"Front Microbiol"},{"issue":"1","key":"pone.0296109.ref039","doi-asserted-by":"crossref","first-page":"fuab049","DOI":"10.1093\/femsre\/fuab049","article-title":"Global colistin use: a review of the emergence of resistant Enterobacterales and the impact on their genetic basis","volume":"46","author":"U Binsker","year":"2022","journal-title":"FEMS Microbiol 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