{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T01:44:25Z","timestamp":1792806265712,"version":"4.5.0"},"reference-count":122,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T00:00:00Z","timestamp":1770249600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Vet. Sci."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Detection of pathogens associated with bovine respiratory disease (BRD) typically involves several laboratory tools, with results limited to a defined list of targets. This study adapted a previously reported method for metagenomic sequencing of nasal swabs to describe sequencing data from BRD associated viruses. Changes in virus composition were identified between arrival to a feedlot and 14 days on feed (DOF). These data were also assessed for the simultaneous characterization of bacteria and antimicrobial resistance genes (ARGs).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Nasal swabs were obtained from fall-placed calves (FPC) and yearlings (YRL) from western Canadian commercial feedlots. Evidence of respiratory viruses were identified by sampling 380 animals during processing on arrival to the feedlot and again after 14 DOF using Nanopore metagenomic sequencing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Twenty-one distinct viruses from 12 viral families were identified, with multiple viruses detected in most samples. In FPC arrival samples, the most common BRD associated viruses were bovine rhinitis B virus (BRBV; 46%), bovine coronavirus (BCoV; 32%), influenza D virus (IDV; 17%), bovine respiratory syncytial virus (BRSV; 8.5%), and bovine parainfluenza virus 3 (BPIV-3; 4.2%). The prevalences of bovine herpesvirus type 1 (BoHV-1; 2.7%), BPIV-3 (12%), BRSV (26%), and IDV (51%) were higher in 14 DOF samples compared to arrival samples (\n                      <jats:italic>p<\/jats:italic>\n                      &amp;lt; 0.05). Bovine viral diarrhea virus 1 (BVDV-1) and 2 (BVDV-2) were rarely detected at either time. The most prevalent viruses detected in YRL arrival samples were BRBV (42%), BRSV (39%), BPIV-3 (20%), IDV (16%), BCoV (12%), and BVDV-2 (7.5%). The prevalences of BRSV (60%), BPIV-3 (39%), and BVDV-2 (17%) were higher in 14 DOF samples than arrival samples (\n                      <jats:italic>p<\/jats:italic>\n                      &amp;lt; 0.05). BRSV (OR 7.0, 1.7\u201329) and BPIV-3 (OR 5.7, 1.5\u201321) were more likely to be detected in arrival samples from YRL than FPC (\n                      <jats:italic>p<\/jats:italic>\n                      = 0.01). In 14 DOF samples, BPIV-3 (OR 4.9, 1.3\u201319,\n                      <jats:italic>p<\/jats:italic>\n                      = 0.02) and BVDV-2 (OR 13, 2.0\u201383,\n                      <jats:italic>p<\/jats:italic>\n                      = 0.01) were identified more frequently in YRL than FPC. These data allowed the identification of respiratory bacteria and 33 ARGs in parallel with assessment of the viral components. The most prevalent bacteria detected in FPC at arrival were\n                      <jats:italic>Mannheimia haemolytica<\/jats:italic>\n                      (35%),\n                      <jats:italic>Histophilus somni<\/jats:italic>\n                      (35%) and\n                      <jats:italic>Pasteurella multocida<\/jats:italic>\n                      (23%). Detection of\n                      <jats:italic>M. haemolytica<\/jats:italic>\n                      increased at 14 DOF (\n                      <jats:italic>p<\/jats:italic>\n                      = 0.02), while\n                      <jats:italic>P. multocida<\/jats:italic>\n                      detection decreased (\n                      <jats:italic>p<\/jats:italic>\n                      = 0.03). At both arrival and 14 DOF in YRL,\n                      <jats:italic>M. haemolytica<\/jats:italic>\n                      was the most prevalent bacterium, followed by\n                      <jats:italic>P. multocida<\/jats:italic>\n                      and\n                      <jats:italic>H. somni<\/jats:italic>\n                      with no significant differences between arrival and 14 DOF samples. ARGs were detected more frequently in the 14 DOF samples than at arrival for both FPC (\n                      <jats:italic>p<\/jats:italic>\n                      = 0.03) and YRL (\n                      <jats:italic>p<\/jats:italic>\n                      = 0.01). The most commonly detected ARGs were associated with resistance to lincosamides and aminoglycosides; however, ARGs associated with other antimicrobials used in cattle including tetracyclines were also identified.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>Changes in the prevalence of BRD associated viruses early in the feeding period reflect transmission and the potential risk of developing the disease. Frequent detection of BCoV, BRSV, and BPIV-3 in newly arrived feedlot cattle suggests the need for improved vaccination before shipping or limitations in existing commercial vaccine preparations.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fvets.2025.1704412","type":"journal-article","created":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T13:35:11Z","timestamp":1770298511000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Prevalences of respiratory viruses and bacteria in Western Canadian commercial feedlot calves detected using a single metagenomic sequencing protocol vary during the first two weeks of arrival and by age group"],"prefix":"10.3389","volume":"12","author":[{"given":"Emmanuel","family":"Donbraye","sequence":"first","affiliation":[{"name":"Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lianne","family":"McLeod","sequence":"additional","affiliation":[{"name":"Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire N.","family":"Carson","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Royal University Hospital","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhijian","family":"Chai","sequence":"additional","affiliation":[{"name":"Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stacey R.","family":"Lacoste","sequence":"additional","affiliation":[{"name":"Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily K.","family":"Herman","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, University of Manitoba","place":["Winnipeg, MB, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. Luke","family":"McCarthy","sequence":"additional","affiliation":[{"name":"Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet E.","family":"Hill","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan E. N.","family":"Erickson","sequence":"additional","affiliation":[{"name":"Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colleen","family":"Pollock","sequence":"additional","affiliation":[{"name":"Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew G.","family":"Links","sequence":"additional","affiliation":[{"name":"Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon J. G.","family":"Otto","sequence":"additional","affiliation":[{"name":"HEAT-AMR (Human-Environment-Animal Transdisciplinary AMR) Research Group, School of Public Health, University of Alberta","place":["Edmonton, AB, Canada"]},{"name":"Centre for Healthy Communities, School of Public Health, University of Alberta","place":["Edmonton, AB, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheryl","family":"Gow","sequence":"additional","affiliation":[{"name":"Canadian Integrated Program for Antimicrobial Resistance Surveillance, Public Health Agency of Canada","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Stothard","sequence":"additional","affiliation":[{"name":"Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta","place":["Edmonton, AB, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John R.","family":"Campbell","sequence":"additional","affiliation":[{"name":"Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheryl L.","family":"Waldner","sequence":"additional","affiliation":[{"name":"Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan","place":["Saskatoon, SK, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,2,5]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.2460\/javma.2001.219.1122","article-title":"Trends in mortality ratios among cattle in US feedlots","volume":"219","author":"Loneragan","year":"2001","journal-title":"J Am Vet Med Assoc"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"skab361","DOI":"10.1093\/jas\/skab361","article-title":"Factors associated with bovine respiratory disease case fatality in feedlot cattle","volume":"100","author":"Blakebrough-Hall","year":"2022","journal-title":"J Anim Sci"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"329","DOI":"10.3389\/fvets.2019.00329","article-title":"Antimicrobial use on 36 beef feedlots in western Canada: 2008-2012","volume":"6","author":"Brault","year":"2019","journal-title":"Front Vet Sci."},{"key":"ref4","first-page":"255","article-title":"Antimicrobial usage in western Canadian cow-calf herds","volume":"60","author":"Waldner","year":"2019","journal-title":"Can Vet J"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1186\/s13567-022-01086-1","article-title":"Understanding the mechanisms of viral and bacterial coinfections in bovine respiratory disease: a comprehensive literature review of experimental evidence","volume":"53","author":"Gaudino","year":"2022","journal-title":"Vet Res"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"1227","DOI":"10.1111\/tbed.14085","article-title":"Influenza D virus in respiratory disease in Canadian, province of Quebec, cattle: relative importance and evidence of new reassortment between different clades","volume":"69","author":"Saegerman","year":"2022","journal-title":"Transbound Emerg Dis"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.vetmic.2012.07.044","article-title":"Transmission dynamics of Mannheimia haemolytica in newly-received beef bulls at fattening operations","volume":"161","author":"Timsit","year":"2013","journal-title":"Vet Microbiol"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1016\/j.cvfa.2020.03.005","article-title":"Bovine respiratory disease diagnosis: what progress has been made in infectious diagnosis?","volume":"36","author":"Pardon","year":"2020","journal-title":"Vet Clin North Am Food Anim Pract"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"1431","DOI":"10.1099\/ijsem.0.003869","article-title":"Necessity and rationale for the proposed name changes in the classification of Mollicutes species. 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