ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization

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dc.contributor.authorLiang, Xiaoen
dc.contributor.authorZhang, Jingyien
dc.contributor.authorKim, Yoonjinen
dc.contributor.authorHo, Joshen
dc.contributor.authorLiu, Kevinen
dc.contributor.authorKeenum, Ishi M.en
dc.contributor.authorGupta, Surajen
dc.contributor.authorDavis, Benjaminen
dc.contributor.authorHepp, Shannon L.en
dc.contributor.authorZhang, Liqingen
dc.contributor.authorXia, Kangen
dc.contributor.authorKnowlton, Katharine F.en
dc.contributor.authorLiao, Jingqiuen
dc.contributor.authorVikesland, Peter J.en
dc.contributor.authorPruden, Amyen
dc.contributor.authorHeath, Lenwood S.en
dc.date.accessioned2023-12-15T17:52:11Zen
dc.date.available2023-12-15T17:52:11Zen
dc.date.issued2023-09-15en
dc.description.abstractAntibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens. A number of computational pipelines are available and under development to support environmental ARG monitoring; the pipeline we present here is promising for general adoption for the purpose of harmonized global monitoring. Specifically, ARGem is a user-friendly pipeline that provides full-service analysis, from the initial DNA short reads to the final visualization of results. The capture of extensive metadata is also facilitated to support comparability across projects and broader monitoring goals. The ARGem pipeline offers efficient analysis of a modest number of samples along with affordable computational components, though the throughput could be increased through cloud resources, based on the user’s configuration. The pipeline components were carefully assessed and selected to satisfy tradeoffs, balancing efficiency and flexibility. It was essential to provide a step to perform short read assembly in a reasonable time frame to ensure accurate annotation of identified ARGs. Comprehensive ARG and mobile genetic element databases are included in ARGem for annotation support. ARGem further includes an expandable set of analysis tools that include statistical and network analysis and supports various useful visualization techniques, including Cytoscape visualization of co-occurrence and correlation networks. The performance and flexibility of the ARGem pipeline is demonstrated with analysis of aquatic metagenomes. The pipeline is freely available at https://github.com/xlxlxlx/ARGem.en
dc.description.versionPublished versionen
dc.format.extent14 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifierARTN 1219297 (Article number)en
dc.identifier.doihttps://doi.org/10.3389/fgene.2023.1219297en
dc.identifier.eissn1664-8021en
dc.identifier.issn1664-8021en
dc.identifier.orcidVikesland, Peter [0000-0003-2654-5132]en
dc.identifier.orcidPruden-Bagchi, Amy [0000-0002-3191-6244]en
dc.identifier.orcidKnowlton, Katharine [0000-0002-7181-4410]en
dc.identifier.orcidHeath, Lenwood [0000-0003-1608-431X]en
dc.identifier.orcidZhang, Liqing [0000-0003-4660-9199]en
dc.identifier.otherPMC10558085en
dc.identifier.other1219297 (PII)en
dc.identifier.pmid37811141en
dc.identifier.urihttps://hdl.handle.net/10919/117206en
dc.identifier.volume14en
dc.language.isoenen
dc.publisherFrontiersen
dc.relation.urihttps://www.ncbi.nlm.nih.gov/pubmed/37811141en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectantibiotic resistance genesen
dc.subjectworkflowen
dc.subjectmetagenomicsen
dc.subjectbioinformaticsen
dc.subjectgenome annotationen
dc.titleARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualizationen
dc.title.serialFrontiers in Geneticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
dcterms.dateAccepted2023-09-01en
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/School of Animal Sciencesen
pubs.organisational-group/Virginia Tech/Engineeringen
pubs.organisational-group/Virginia Tech/Engineering/Civil & Environmental Engineeringen
pubs.organisational-group/Virginia Tech/Engineering/Computer Scienceen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineering/COE T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen

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