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Metagenomic tracking of antibiotic resistance genes through a pre-harvest vegetable production system: an integrated lab-, microcosm- and greenhouse-scale analysis

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dc.contributor.authorKeenum, Ishi M.en
dc.contributor.authorWind, Lauren L.en
dc.contributor.authorRay, Partha P.en
dc.contributor.authorGuron, Giselle K. P.en
dc.contributor.authorChen, Chaoqien
dc.contributor.authorKnowlton, Katharine F.en
dc.contributor.authorPonder, Monica A.en
dc.contributor.authorPruden, Amyen
dc.date.accessioned2023-01-31T18:34:55Zen
dc.date.available2023-01-31T18:34:55Zen
dc.date.issued2022-05-18en
dc.date.updated2023-01-31T18:13:30Zen
dc.description.abstractPrior research demonstrated the potential for agricultural production systems to contribute to the environmental spread of antibiotic resistance genes (ARGs). However, there is a need for integrated assessment of critical management points for minimizing this potential. Shotgun metagenomic sequencing data were analysed to comprehensively compare total ARG profiles characteristic of amendments (manure or compost) derived from either beef or dairy cattle (with and without dosing antibiotics according to conventional practice), soil (loamy sand or silty clay loam) and vegetable (lettuce or radish) samples collected across studies carried out at laboratory-, microcosm- and greenhouse-scale. Vegetables carried the greatest diversity of ARGs (n = 838) as well as the most ARG-mobile genetic element co-occurrences (n = 945). Radishes grown in manure- or compost-amended soils harboured a higher relative abundance of total (0.91 and 0.91 ARGs/16S rRNA gene) and clinically relevant ARGs than vegetables from other experimental conditions (average: 0.36 ARGs/16S rRNA gene). Lettuce carried the highest relative abundance of pathogen gene markers among the metagenomes examined. Total ARG relative abundances were highest on vegetables grown in loamy sand receiving antibiotic-treated beef amendments. The findings emphasize that additional barriers, such as post-harvest processes, merit further study to minimize potential exposure to consumers.en
dc.description.versionPublished versionen
dc.format.extent17 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1111/1462-2920.16022en
dc.identifier.eissn1462-2920en
dc.identifier.issn1462-2912en
dc.identifier.issue8en
dc.identifier.orcidPruden-Bagchi, Amy [0000-0002-3191-6244]en
dc.identifier.orcidKnowlton, Katharine [0000-0002-7181-4410]en
dc.identifier.orcidPonder, Monica [0000-0001-7047-3127]en
dc.identifier.pmid35466491en
dc.identifier.urihttp://hdl.handle.net/10919/113593en
dc.identifier.volume24en
dc.language.isoenen
dc.publisherWileyen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000797240300001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectantimicrobial resistanceen
dc.subjectmanure applicationen
dc.subjectdairy manureen
dc.subjectsoilen
dc.subjectabundanceen
dc.subjectresistomeen
dc.subjectbacteriaen
dc.subjectdatabaseen
dc.subjectimpacten
dc.subjectfertilizationen
dc.subjectgeneticsen
dc.subject.meshAnimalsen
dc.subject.meshCattleen
dc.subject.meshLettuceen
dc.subject.meshVegetablesen
dc.subject.meshRNA, Ribosomal, 16Sen
dc.subject.meshManureen
dc.subject.meshSoilen
dc.subject.meshAnti-Bacterial Agentsen
dc.subject.meshSoil Microbiologyen
dc.subject.meshDrug Resistance, Microbialen
dc.subject.meshGenes, Bacterialen
dc.subject.meshMetagenomeen
dc.subject.meshSanden
dc.titleMetagenomic tracking of antibiotic resistance genes through a pre-harvest vegetable production system: an integrated lab-, microcosm- and greenhouse-scale analysisen
dc.title.serialEnvironmental Microbiologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherEarly Accessen
dc.type.otherJournalen
dcterms.dateAccepted2022-04-18en
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/Agriculture & Life Sciences/Food Science and Technologyen
pubs.organisational-group/Virginia Tech/Engineeringen
pubs.organisational-group/Virginia Tech/Engineering/Civil & Environmental Engineeringen
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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