{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T23:34:56Z","timestamp":1785540896228,"version":"3.56.0"},"reference-count":79,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T00:00:00Z","timestamp":1614038400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","award":["Agriculture and Food Research Initiative\u2019s Competitive Grant 2017\u201068003\u201026499"],"award-info":[{"award-number":["Agriculture and Food Research Initiative\u2019s Competitive Grant 2017\u201068003\u201026499"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009227","name":"Iowa State University","doi-asserted-by":"publisher","award":["Antimicrobial Resistance Consortium"],"award-info":[{"award-number":["Antimicrobial Resistance Consortium"]}],"id":[{"id":"10.13039\/100009227","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R44AI122654 and R44AI150008"],"award-info":[{"award-number":["R44AI122654 and R44AI150008"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1195084"],"award-info":[{"award-number":["OPP1195084"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with \u226580% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.<\/jats:p>","DOI":"10.3390\/antibiotics10020221","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T12:40:16Z","timestamp":1614084016000},"page":"221","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7223-0409","authenticated-orcid":false,"given":"Ashenafi F.","family":"Beyi","sequence":"first","affiliation":[{"name":"Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan","family":"Hassall","sequence":"additional","affiliation":[{"name":"Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0048-512X","authenticated-orcid":false,"given":"Gregory J.","family":"Phillips","sequence":"additional","affiliation":[{"name":"Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5784-8382","authenticated-orcid":false,"given":"Paul J.","family":"Plummer","sequence":"additional","affiliation":[{"name":"Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA"},{"name":"Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA"},{"name":"National Institute of Antimicrobial Resistance Research and Education, Ames, IA 50010, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,2,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"637","DOI":"10.3168\/jds.2017-12867","article-title":"Farm-specific economic value of automatic lameness detection systems in dairy cattle: From concepts to operational simulations","volume":"101","author":"Saeys","year":"2018","journal-title":"J. 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