{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T13:55:09Z","timestamp":1791381309616,"version":"4.3.3"},"reference-count":33,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T00:00:00Z","timestamp":1763424000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"\n Background<\/jats:title>\n \n Mobile colistin resistance (MCR) genes, have been increasingly identified worldwide, but their presence and characteristics in Africa remain poorly understood. Herein, we characterized a silent\n mcr-9<\/jats:italic>\n gene carried in\n Enterobacteriaceae<\/jats:italic>\n from Ethiopia.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n In a study investigating genomic epidemiology of ESBL-producing Gram-negative bacilli from clinical samples in 2016, eleven isolates were found to encode\n mcr-9<\/jats:italic>\n genes. Whole genome sequencing, combining Illumina and MinION Nanopore technologies were performed for in-depth investigation of the genome and understand the genetic contexts of\n mcr-9<\/jats:italic>\n and its associated plasmids.\n <\/jats:p>\n <\/jats:sec>\n \n Result<\/jats:title>\n \n The\n mcr-9<\/jats:italic>\n genes were detected in\n Enterobacter cloacae<\/jats:italic>\n (n\u2009=\u20098),\n Escherichia coli<\/jats:italic>\n (n\u2009=\u20091),\n Klebsiella pneumoniae<\/jats:italic>\n (n\u2009=\u20091), and\n K. michiganensis<\/jats:italic>\n (n\u2009=\u20091). They were isolated from urine (54.5%, 6\/11), wound secretions (27.3%, 3\/11), and fecal samples (n\u2009=\u200918.2%, 2\/11). In addition to\n mcr-9<\/jats:italic>\n , all isolates encoded\n bla<\/jats:italic>\n CTX-M-15<\/jats:sub>\n , and\n aac (6\u2019)-Ib-cr<\/jats:italic>\n among several other resistance genes. These isolates were susceptible\u00a0to colistin (MIC\u2009\u2264\u20090.5 mg\/L). The\n E. cloacae<\/jats:italic>\n strains belong to three different sequence types (ST): ST114 (n\u2009=\u20093), ST184 (n\u2009=\u20093), ST254 (n\u2009=\u20091), and\n Enterobacter mori<\/jats:italic>\n ST2197 (n\u2009=\u20091)), whereas the\n E. coli<\/jats:italic>\n and the\n K. pneumoniae<\/jats:italic>\n strains belonged to ST410 and ST337.\n IncHI2<\/jats:italic>\n and\n IncHI2<\/jats:italic>\n A plasmid replicons were present in all isolates. Although the genetic content of plasmids carrying the\n mcr-9<\/jats:italic>\n genes varied, the genetic contexts surrounding all\n mcr<\/jats:italic>\n genes within \u00b110kb region were largely consistent, mostly flanked by composite transposons such as IS\n 26<\/jats:italic>\n , and IS\n 903B<\/jats:italic>\n .\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n A silent\n mcr-9<\/jats:italic>\n gene was detected among ESBL-producing\n Enterobacteriaceae<\/jats:italic>\n isolates. The\n IncHI2<\/jats:italic>\n plasmids encoding the\n mcr-9<\/jats:italic>\n had 25% genetic content dissimilarity.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.1371\/journal.pone.0336440","type":"journal-article","created":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T18:23:30Z","timestamp":1763490210000},"page":"e0336440","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Silent spread of mcr-9 in ESBL-producing Enterobacteriaceae clinical isolates, Jimma, Ethiopia"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8295-2106","authenticated-orcid":true,"given":"Tsegaye","family":"Sewunet","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Razavi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaitanya","family":"Tellapragada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian G.","family":"Giske","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,11,18]]},"reference":[{"issue":"1","key":"pone.0336440.ref001","doi-asserted-by":"crossref","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":"M Acman","year":"2022","journal-title":"Nat Commun"},{"issue":"9","key":"pone.0336440.ref002","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nrmicro1235","article-title":"Mobile genetic elements: the agents of open source evolution","volume":"3","author":"LS Frost","year":"2005","journal-title":"Nat Rev Microbiol"},{"key":"pone.0336440.ref003","first-page":"1","article-title":"Selfish, promiscuous, and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations","author":"M Haudiquet","year":"2021","journal-title":"EvoEcoRxiv"},{"key":"pone.0336440.ref004","author":"WHO Advisory Group"},{"issue":"3","key":"pone.0336440.ref005","doi-asserted-by":"crossref","first-page":"365","DOI":"10.5644\/ama2006-124.355","article-title":"mcr Genes Conferring Colistin Resistance in Enterobacterales; a Five Year Overview","volume":"50","author":"M Chatzidimitriou","year":"2021","journal-title":"Acta Med Acad"},{"key":"pone.0336440.ref006","doi-asserted-by":"crossref","first-page":"941358","DOI":"10.3389\/fcimb.2022.941358","article-title":"Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update","volume":"12","author":"M Mmatli","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"key":"pone.0336440.ref007","first-page":"1","article-title":"Identification of novel mobilized colistin resistance gene mcr-9 in a multidrug-resistant, colistin-susceptible Salmonella enterica serotype Typhimurium","volume":"10","author":"LM Carroll","year":"2019","journal-title":"J Antimicrobial Chemotherapy"},{"issue":"9","key":"pone.0336440.ref008","doi-asserted-by":"crossref","first-page":"e00965","DOI":"10.1128\/AAC.00965-19","article-title":"mcr-9, an Inducible Gene Encoding an Acquired Phosphoethanolamine Transferase in Escherichia coli, and Its Origin","volume":"63","author":"N Kieffer","year":"2019","journal-title":"Antimicrob Agents Chemother"},{"key":"pone.0336440.ref009","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.jgar.2021.10.022","article-title":"Global prevalence and molecular epidemiology of mcr-mediated colistin resistance in Escherichia coli clinical isolates: a systematic review","volume":"29","author":"M Dadashi","year":"2022","journal-title":"J Glob Antimicrob Resist"},{"issue":"10","key":"pone.0336440.ref010","doi-asserted-by":"crossref","first-page":"461","DOI":"10.3390\/microorganisms7100461","article-title":"Global burden of colistin-resistant bacteria: mobilized colistin resistance genes study (1980-2018)","volume":"7","author":"M Elbediwi","year":"2019","journal-title":"Microorganisms"},{"issue":"2","key":"pone.0336440.ref011","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1007\/s15010-019-01377-4","article-title":"Bloodstream infections caused by Escherichia coli carrying mcr-1 gene in hospitalized patients in northern Italy from 2012 to 2018","volume":"48","author":"B Mariani","year":"2020","journal-title":"Infection"},{"issue":"10","key":"pone.0336440.ref012","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1093\/cid\/ciw124","article-title":"Plasmid-Mediated Colistin-Resistant Escherichia coli in Bacteremia in Switzerland","volume":"62","author":"P Nordmann","year":"2016","journal-title":"Clin Infect Dis"},{"issue":"1","key":"pone.0336440.ref013","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1080\/22221751.2020.1717380","article-title":"Colistin-resistance gene mcr in clinical carbapenem-resistant Enterobacteriaceae strains in China, 2014-2019","volume":"9","author":"H Huang","year":"2020","journal-title":"Emerg Microbes Infect"},{"key":"pone.0336440.ref014","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.jgar.2019.12.018","article-title":"First report of the mcr-1 colistin resistance gene identified in two Escherichia coli isolates from clinical samples, Philippines, 2018","volume":"21","author":"JMS Velasco","year":"2020","journal-title":"J Glob Antimicrob Resist"},{"issue":"6","key":"pone.0336440.ref015","doi-asserted-by":"crossref","first-page":"e01008","DOI":"10.1128\/mSphere.01008-20","article-title":"Detection of five mcr-9-carrying enterobacterales isolates in four czech hospitals","volume":"5","author":"I Bitar","year":"2020","journal-title":"mSphere"},{"key":"pone.0336440.ref016","doi-asserted-by":"crossref","first-page":"105326","DOI":"10.1016\/j.ebiom.2024.105326","article-title":"Decoding the origins, spread, and global risks of mcr-9 gene","volume":"108","author":"K Song","year":"2024","journal-title":"EBioMedicine"},{"key":"pone.0336440.ref017","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/j.jgar.2021.09.017","article-title":"Polyclonal spread of blaCTX-M-15 through high-risk clones of Escherichia coli at a tertiary hospital in Ethiopia","volume":"29","author":"T Sewunet","year":"2022","journal-title":"J Glob Antimicrob Resist"},{"issue":"1","key":"pone.0336440.ref018","doi-asserted-by":"crossref","first-page":"dlab001","DOI":"10.1093\/jacamr\/dlab001","article-title":"High prevalence of blaCTX-M-15 and nosocomial transmission of hypervirulent epidemic clones of Klebsiella pneumoniae at a tertiary hospital in Ethiopia","volume":"3","author":"T Sewunet","year":"2021","journal-title":"JAC Antimicrob Resist"},{"key":"pone.0336440.ref019","unstructured":"K F, Galore T. A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. 2015;516(517)."},{"key":"pone.0336440.ref020","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pone.0336440.ref021","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1007\/s10096-020-04003-6","article-title":"Citrobacter telavivum sp. nov. with chromosomal mcr-9 from hospitalized patients","volume":"40","author":"TG Ribeiro","year":"2021","journal-title":"Eur J Clin Microbiol Infect Dis"},{"issue":"8","key":"pone.0336440.ref022","doi-asserted-by":"crossref","first-page":"e00573","DOI":"10.1128\/AAC.00573-20","article-title":"The mcr-9 gene of salmonella and escherichia coli is not associated with colistin resistance in the United States","volume":"64","author":"GH Tyson","year":"2020","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"pone.0336440.ref023","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/s41467-022-35717-0","article-title":"Resolving colistin resistance and heteroresistance in Enterobacter species","volume":"14","author":"SP Doijad","year":"2023","journal-title":"Nat Commun"},{"key":"pone.0336440.ref024","doi-asserted-by":"crossref","first-page":"756201","DOI":"10.3389\/fmicb.2021.756201","article-title":"Co-occurrence of blaNDM-1 and mcr-9 in a Conjugative IncHI2\/HI2A Plasmid From a Bloodstream Infection-Causing Carbapenem-Resistant Klebsiella pneumoniae","volume":"12","author":"Z Liu","year":"2021","journal-title":"Front Microbiol"},{"key":"pone.0336440.ref025","doi-asserted-by":"crossref","unstructured":"Lee KY, Hopkins JD, Syvanen M. Direct involvement of IS26 in an antibiotic resistance operon. 1990;172.","DOI":"10.1128\/jb.172.6.3229-3236.1990"},{"issue":"8","key":"pone.0336440.ref026","doi-asserted-by":"crossref","first-page":"e0053422","DOI":"10.1128\/aac.00534-22","article-title":"Genomic epidemiology of carbapenemase-producing and colistin-resistant enterobacteriaceae among sepsis patients in Ethiopia: a whole-genome analysis","volume":"66","author":"MH Legese","year":"2022","journal-title":"Antimicrob Agents Chemother"},{"issue":"6","key":"pone.0336440.ref027","doi-asserted-by":"crossref","first-page":"e00897","DOI":"10.1128\/mSystems.00897-20","article-title":"Genomic and resistance epidemiology of gram-negative bacteria in Africa: a systematic review and phylogenomic analyses from a one health perspective","volume":"5","author":"J Osei Sekyere","year":"2020","journal-title":"mSystems"},{"key":"pone.0336440.ref028","doi-asserted-by":"crossref","unstructured":"Sadek M, Nariya H, Shimamoto T. First genomic characterization of bla VIM-1 and mcr-9- coharbouring Enterobacter hormaechei. 2020;:1\u20137.","DOI":"10.3390\/pathogens9090687"},{"key":"pone.0336440.ref029","doi-asserted-by":"crossref","first-page":"6630379","DOI":"10.1155\/2021\/6630379","article-title":"Prevalence and Traits of Mobile Colistin Resistance Gene Harbouring Isolates from Different Ecosystems in Africa","volume":"2021","author":"MU Anyanwu","year":"2021","journal-title":"Biomed Res Int"},{"issue":"1","key":"pone.0336440.ref030","doi-asserted-by":"crossref","first-page":"8113","DOI":"10.1038\/s41598-020-65106-w","article-title":"Characterization of the global distribution and diversified plasmid reservoirs of the colistin resistance gene mcr-9","volume":"10","author":"Y Li","year":"2020","journal-title":"Sci Rep"},{"key":"pone.0336440.ref031","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.2147\/IDR.S248342","article-title":"Co-Occurrence of mcr-9 and blaNDM-1 in Enterobacter cloacae Isolated from a Patient with Bloodstream Infection","volume":"13","author":"M Lin","year":"2020","journal-title":"Infect Drug Resist"},{"key":"pone.0336440.ref032","unstructured":"Babiker A, Bower C, Lutgring JD. Clinical and genomic epidemiology of mcr-9 -carrying carbapenem-resistant Enterobacterales isolates in metropolitan. 2017."},{"key":"pone.0336440.ref033","doi-asserted-by":"crossref","first-page":"705230","DOI":"10.3389\/fmicb.2021.705230","article-title":"Emergence of IncHI2 plasmids with mobilized colistin resistance (mcr)-9 gene in ESBL-producing, multidrug-resistant salmonella typhimurium and Its monophasic variant ST34 from food-producing animals in italy","volume":"12","author":"EL Diaconu","year":"2021","journal-title":"Front Microbiol"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0336440","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T18:23:34Z","timestamp":1763490214000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0336440"}},"subtitle":[],"editor":[{"given":"Md Bashir","family":"Uddin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,11,18]]},"references-count":33,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2025,11,18]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0336440","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,18]]}}}