{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,26]],"date-time":"2026-07-26T04:07:10Z","timestamp":1785038830139,"version":"3.55.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T00:00:00Z","timestamp":1668556800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"School of Veterinary Medicine and Biomedical Sciences Texas A&M University"},{"name":"Minnesota Agricultural Research, Education and Extension Technology Transfer Program"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01-AI141810"],"award-info":[{"award-number":["R01-AI141810"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Antimicrobial resistance (AMR) is considered a critical threat to public health, and genomic\/metagenomic investigations featuring high-throughput analysis of sequence data are increasingly common and important. We previously introduced MEGARes, a comprehensive AMR database with an acyclic hierarchical annotation structure that facilitates high-throughput computational analysis, as well as AMR++, a customized bioinformatic pipeline specifically designed to use MEGARes in high-throughput analysis for characterizing AMR genes (ARGs) in metagenomic sequence data. Here, we present MEGARes v3.0, a comprehensive database of published ARG sequences for antimicrobial drugs, biocides, and metals, and AMR++ v3.0, an update to our customized bioinformatic pipeline for high-throughput analysis of metagenomic data (available at MEGLab.org). Database annotations have been expanded to include information regarding specific genomic locations for single-nucleotide polymorphisms (SNPs) and insertions and\/or deletions (indels) when required by specific ARGs for resistance expression, and the updated AMR++ pipeline uses this information to check for presence of resistance-conferring genetic variants in metagenomic sequenced reads. This new information encompasses 337 ARGs, whose resistance-conferring variants could not previously be confirmed in such a manner. In MEGARes 3.0, the nodes of the acyclic hierarchical ontology include 4 antimicrobial compound types, 59 resistance classes, 233 mechanisms\u00a0and 1448 gene groups that classify the 8733 accessions.<\/jats:p>","DOI":"10.1093\/nar\/gkac1047","type":"journal-article","created":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T08:20:30Z","timestamp":1668586830000},"page":"D744-D752","source":"Crossref","is-referenced-by-count":200,"title":["MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing"],"prefix":"10.1093","volume":"51","author":[{"given":"Nathalie","family":"Bonin","sequence":"first","affiliation":[{"name":"Department of Computer and Information Science and Engineering, University of Florida , Gainesville, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrique","family":"Doster","sequence":"additional","affiliation":[{"name":"VERO Program, Veterinary Medicine and Biomedical Sciences, Texas A&M University , Canyon, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Worley","sequence":"additional","affiliation":[{"name":"Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota , St. Paul, MN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lee J","family":"Pinnell","sequence":"additional","affiliation":[{"name":"VERO Program, Veterinary Medicine and Biomedical Sciences, Texas A&M University , Canyon, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan E","family":"Bravo","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Science and Engineering, University of Florida , Gainesville, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Ferm","sequence":"additional","affiliation":[{"name":"Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota , St. Paul, MN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5704-3533","authenticated-orcid":false,"given":"Simone","family":"Marini","sequence":"additional","affiliation":[{"name":"Data Intelligence Systems Lab, Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida , Gainesville, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9021-5595","authenticated-orcid":false,"given":"Mattia","family":"Prosperi","sequence":"additional","affiliation":[{"name":"Data Intelligence Systems Lab, Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida , Gainesville, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noelle","family":"Noyes","sequence":"additional","affiliation":[{"name":"Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota , St. Paul, MN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul S","family":"Morley","sequence":"additional","affiliation":[{"name":"VERO Program, Veterinary Medicine and Biomedical Sciences, Texas A&M University , Canyon, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9509-9725","authenticated-orcid":false,"given":"Christina","family":"Boucher","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Science and Engineering, University of Florida , Gainesville, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,16]]},"reference":[{"key":"2023010804311950100_B1","doi-asserted-by":"crossref","first-page":"D574","DOI":"10.1093\/nar\/gkw1009","article-title":"MEGARes: an antimicrobial resistance database for high throughput sequencing","volume":"45","author":"Lakin","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2023010804311950100_B2","doi-asserted-by":"crossref","first-page":"D561","DOI":"10.1093\/nar\/gkz1010","article-title":"MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data","volume":"48","author":"Doster","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2023010804311950100_B3","doi-asserted-by":"crossref","first-page":"9149","DOI":"10.1021\/acs.est.1c08918","article-title":"Antimicrobial resistance monitoring of water environments: a framework for standardized methods and quality control","volume":"56","author":"Liguori","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"2023010804311950100_B4","doi-asserted-by":"crossref","first-page":"e0064622","DOI":"10.1128\/aem.00646-22","article-title":"Genomic analysis of carbapenem-resistant comamonas in water matrices: implications for public health and wastewater treatments","volume":"88","author":"Hem","year":"2022","journal-title":"Appl. Environ. Microbiol."},{"key":"2023010804311950100_B5","doi-asserted-by":"crossref","first-page":"109821","DOI":"10.1016\/j.ijfoodmicro.2022.109821","article-title":"Multidrug resistance and virulence genes carried by mobile genomic elements in Salmonella enterica isolated from live food animals, processed, and retail meat in North Carolina, 2018\u20132019","volume":"378","author":"Hull","year":"2022","journal-title":"Int. J. Food Microbiol."},{"key":"2023010804311950100_B6","doi-asserted-by":"crossref","first-page":"734649","DOI":"10.3389\/fmicb.2021.734649","article-title":"Whole genome sequencing of Extended-Spectrum- and AmpC- \u03b2-lactamase-positive enterobacterales isolated from spinach production in Gauteng Province, South Africa","volume":"12","author":"Richter","year":"2021","journal-title":"Front. Microbiol."},{"key":"2023010804311950100_B7","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1007\/s12275-022-1616-z","article-title":"Whole-genome sequencing analysis of Shiga toxin-producing Escherichia coli O22:H8 isolated from cattle prediction pathogenesis and colonization factors and position in STEC universe phylogeny","volume":"60","author":"Da\u00a0Silva","year":"2022","journal-title":"J. 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