HT-ARGfinder: A Comprehensive Pipeline for Identifying Horizontally Transferred Antibiotic Resistance Genes and Directionality in Metagenomic Sequencing Data

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dc.contributor.authorDas, Badhanen
dc.contributor.authorEmon, Muhit Islamen
dc.contributor.authorMoumi, Nazifa Ahmeden
dc.contributor.authorSein, Justinen
dc.contributor.authorPruden, Amyen
dc.contributor.authorHeath, Lenwood S.en
dc.contributor.authorZhang, Liqingen
dc.date.accessioned2022-12-13T16:03:20Zen
dc.date.available2022-12-13T16:03:20Zen
dc.date.issued2022-06en
dc.description.abstractAntibiotic resistance is a continually rising threat to global health. A primary driver of the evolution of new strains of resistant pathogens is the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). However, identifying and quantifying ARGs subject to HGT remains a significant challenge. Here, we introduce HT-ARGfinder (horizontally transferred ARG finder), a pipeline that detects and enumerates horizontally transferred ARGs in metagenomic data while also estimating the directionality of transfer. To demonstrate the pipeline, we applied it to an array of publicly-available wastewater metagenomes, including hospital sewage. We compare the horizontally transferred ARGs detected across various sample types and estimate their directionality of transfer among donors and recipients. This study introduces a comprehensive tool to track mobile ARGs in wastewater and other aquatic environments.en
dc.description.notesFunding This work was supported in part by the U.S. National Science Foundation Awards 1545756, 2004751, and 2125798.en
dc.description.sponsorshipU.S. National Science Foundation [1545756, 2004751, 2125798]en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3389/fenvs.2022.901917en
dc.identifier.eissn2296-665Xen
dc.identifier.other901917en
dc.identifier.urihttp://hdl.handle.net/10919/112869en
dc.identifier.volume10en
dc.language.isoenen
dc.publisherFrontiersen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectantibiotic resistance geneen
dc.subjecthorizontal gene transferen
dc.subjectmetagenomicsen
dc.subjecturban conventional activated sludgeen
dc.subjecthospital sewageen
dc.subjecturban sewageen
dc.titleHT-ARGfinder: A Comprehensive Pipeline for Identifying Horizontally Transferred Antibiotic Resistance Genes and Directionality in Metagenomic Sequencing Dataen
dc.title.serialFrontiers in Environmental Scienceen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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