{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T05:18:18Z","timestamp":1790745498308,"version":"4.1.0"},"reference-count":79,"publisher":"Microbiology Society","issue":"3","license":[{"start":{"date-parts":[[2023,3,24]],"date-time":"2023-03-24T00:00:00Z","timestamp":1679616000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003329","name":"Ministerio de Econom\u00eda y Competitividad","doi-asserted-by":"crossref","award":["BES-2015-073164"],"award-info":[{"award-number":["BES-2015-073164"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100012818","name":"Comunidad de Madrid","doi-asserted-by":"crossref","award":["REACT-EU"],"award-info":[{"award-number":["REACT-EU"]}],"id":[{"id":"10.13039\/100012818","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,24]]},"abstract":"<jats:p>Antimicrobial resistance (AMR) mechanisms, especially those conferring resistance to critically important antibiotics, are a great concern for public health. 16S rRNA methyltransferases (16S-RMTases) abolish the effectiveness of most clinically used aminoglycosides, but some of them are considered sporadic, such as RmtE. The main goals of this work were the genomic analysis of bacteria producing 16S-RMTases from a \u2018One Health\u2019 perspective in Venezuela, and the study of the epidemiological and evolutionary scenario of RmtE variants and their related mobile genetic elements (MGEs) worldwide. A total of 21\u2009samples were collected in 2014 from different animal and environmental sources in the Cuman\u00e1 region (Venezuela). Highly aminoglycoside-resistant <jats:italic>\n                     <jats:named-content content-type=\"family\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3091\" xlink:type=\"simple\">Enterobacteriaceae<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> isolates were selected, identified and screened for 16S-RMTase genes. Illumina and Nanopore whole-genome sequencing data were combined to obtain hybrid assemblies and analyse their sequence type, resistome, plasmidome and pan-genome. Genomic collections of <jats:italic>rmtE<\/jats:italic> variants and their associated MGEs were generated to perform epidemiological and phylogenetic analyses. A single 16S-RMTase, the novel RmtE4, was identified in five <jats:italic>\n                     <jats:named-content content-type=\"genus\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3202\" xlink:type=\"simple\">Klebsiella<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> isolates from wastewater samples of Cuman\u00e1. This variant possessed three amino acid modifications with respect to RmtE1\u20133 (Asn152Asp, Val216Ile and Lys267Ile), representing the most genetic distant among all known and novel variants described in this work, and the second most prevalent. <jats:italic>rmtE<\/jats:italic> variants were globally spread, and their geographical distribution was determined by the associated MGEs and the carrying bacterial species. Thus, <jats:italic>rmtE4<\/jats:italic> was found to be confined to <jats:italic>\n                     <jats:named-content content-type=\"genus\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.3202\" xlink:type=\"simple\">Klebsiella<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> isolates from South America, where it was closely related to IS<jats:italic>Vsa3<\/jats:italic> and an uncommon IncL plasmid related with hospital environments. This work uncovered the global scenario of RmtE and the existence of RmtE4, which could potentially emerge from South America. Surveillance and control measures should be developed based on these findings in order to prevent the dissemination of this AMR mechanism and preserve public health worldwide.<\/jats:p>","DOI":"10.1099\/mgen.0.000946","type":"journal-article","created":{"date-parts":[[2023,3,24]],"date-time":"2023-03-24T15:16:28Z","timestamp":1679670988000},"source":"Crossref","is-referenced-by-count":4,"title":["Global scenario of the RmtE pan-aminoglycoside-resistance mechanism: emergence of the rmtE4 gene in South America associated with a hospital-related IncL plasmid"],"prefix":"10.1099","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6447-7113","authenticated-orcid":false,"given":"Jose F.","family":"Delgado-Blas","sequence":"first","affiliation":[{"name":"Antimicrobial Resistance Unit (ARU), Animal Health Department, Faculty of Veterinary Medicine and VISAVET Health Surveillance Centre, Complutense University of Madrid (UCM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina M.","family":"Ovejero","sequence":"additional","affiliation":[{"name":"Antimicrobial Resistance Unit (ARU), Animal Health Department, Faculty of Veterinary Medicine and VISAVET Health Surveillance Centre, Complutense University of Madrid (UCM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophia","family":"David","sequence":"additional","affiliation":[{"name":"Centre for Genomic Pathogen Surveillance (CGPS), Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6008-6024","authenticated-orcid":false,"given":"Carlos","family":"Serna","sequence":"additional","affiliation":[{"name":"Antimicrobial Resistance Unit (ARU), Animal Health Department, Faculty of Veterinary Medicine and VISAVET Health Surveillance Centre, Complutense University of Madrid (UCM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Pulido-Vadillo","sequence":"additional","affiliation":[{"name":"Antimicrobial Resistance Unit (ARU), Animal Health Department, Faculty of Veterinary Medicine and VISAVET Health Surveillance Centre, Complutense University of Madrid (UCM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Montero","sequence":"additional","affiliation":[{"name":"Antimicrobial Resistance Unit (ARU), Animal Health Department, Faculty of Veterinary Medicine and VISAVET Health Surveillance Centre, Complutense University of Madrid (UCM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Aanensen","sequence":"additional","affiliation":[{"name":"Centre for Genomic Pathogen Surveillance (CGPS), Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorena","family":"Abadia-Pati\u00f1o","sequence":"additional","affiliation":[{"name":"Bacterial Resistance Laboratory, Department of Biomedicine, Institute for Research in Biomedicine and Applied Sciences, University of Oriente (IIBCAUDO), Cuman\u00e1, Venezuela"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6958-4716","authenticated-orcid":false,"given":"Bruno","family":"Gonzalez-Zorn","sequence":"additional","affiliation":[{"name":"Antimicrobial Resistance Unit (ARU), Animal Health Department, Faculty of Veterinary Medicine and VISAVET Health Surveillance Centre, Complutense University of Madrid (UCM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a027029"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.51.3.341-350.1987"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.83.16.6164"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1039\/c2np20092a"},{"key":"R5","volume-title":"Critically Important Antimicrobials for Human Medicine, 6th Revision (https:\/\/www.who.int\/publications\/i\/item\/9789241515528)","year":"2019"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1016\/j.drup.2010.08.003"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1002\/phar.2203"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(87)90349-4"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1016\/j.drup.2012.05.001"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1016\/j.idc.2020.06.002"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01009-21"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01743-09"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00852-15"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.3201\/eid2305.162000"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02397-18"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00054-20"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-020-05264-4"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01235-15"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.001531"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1016\/j.idc.2016.02.011"},{"key":"R21","article-title":"Breakpoint Tables for Interpretation of MICs and Zone Diameters, version 9.0. V\u00e4xj\u00f6: European Committee on Antimicrobial Susceptibility Testing","year":"2019"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2017.0300"},{"key":"R23","article-title":"FastQC: a Quality Control Analysis Tool for High Throughput Sequencing Data","author":"Andrews","year":"2019"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R25","article-title":"Porechop","author":"Wick","year":"2019"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"R28","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv383"},{"key":"R29","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"R31","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dks261"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-3-r46"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx1095"},{"key":"R35","doi-asserted-by":"publisher","DOI":"10.21105\/joss.00118"},{"key":"R36","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000131"},{"key":"R37","article-title":"ABRicate","author":"Seemann","year":"2020"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24448-3"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000056"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033"},{"key":"R42","article-title":"FigTree","author":"Rambaut","year":"2019"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts199"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000093"},{"key":"R45","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2289704"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/22.22.4673"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj014"},{"key":"R48","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr039"},{"key":"R49","article-title":"R: a Language and Environment for Statistical Computing","year":"2019"},{"key":"R50","article-title":"RStudio: Integrated Development Environment for R. RStudio","year":"2019"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv428"},{"key":"R52","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"Ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol Evol"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v040.i01"},{"key":"R54","article-title":"Data.table: Extension of data.frame, R package version","author":"Dowle","year":"2019;1(8)"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0123063"},{"key":"R56","doi-asserted-by":"publisher","DOI":"10.1016\/j.plasmid.2020.102528"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196"},{"key":"R58","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx610"},{"key":"R59","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn179"},{"key":"R60","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2013.0193"},{"key":"R61","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268814000995"},{"key":"R62","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00020-12"},{"key":"R63","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01775-15"},{"key":"R64","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0315-1"},{"key":"R65","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00022-08"},{"key":"R66","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3399"},{"key":"R67","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02829-17"},{"key":"R68","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0445-2"},{"key":"R69","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00588-21","article-title":"A SXT\/R391 integrative and conjugative element carries two copies of the blandm-1gene in Proteus mirabilis","volume":"6","author":"He","year":"2021","journal-title":"mSphere"},{"key":"R70","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.01019-21"},{"key":"R71","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jix524"},{"key":"R72","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02011-17"},{"key":"R73","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2021.09.013"},{"key":"R74","doi-asserted-by":"publisher","DOI":"10.1016\/j.nmni.2015.02.007"},{"key":"R75","doi-asserted-by":"publisher","DOI":"10.1016\/j.envint.2020.105689"},{"key":"R76","doi-asserted-by":"publisher","DOI":"10.1016\/j.envpol.2022.119437"},{"key":"R77","doi-asserted-by":"publisher","DOI":"10.1186\/s12199-021-01023-2"},{"key":"R78","doi-asserted-by":"publisher","DOI":"10.2166\/wh.2020.033"},{"key":"R79","doi-asserted-by":"publisher","DOI":"10.1021\/es505521w"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000946?crawler=true","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,24]],"date-time":"2023-03-24T15:16:34Z","timestamp":1679670994000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000946"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,24]]},"references-count":79,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,3,24]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000946","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,24]]}}}