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

Emmanuel Donbraye¹Lianne McLeod¹Claire N. Carson²Zhijian Chai¹Stacey R. Lacoste¹Emily K. Herman³E. Luke McCarthy⁴Janet E. Hill⁵Nathan E.N. Erickson¹Colleen Pollock¹Matthew G. Links⁴Simon J.G. Otto^6,7Sheryl Gow⁸Paul Stothard⁹John R. Campbell¹Cheryl L. Waldner^1*

• ¹Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
• ²Department of Laboratory Medicine, Royal University Hospital, Saskatoon, Canada
• ³Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
• ⁴Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Canada
• ⁵Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
• ⁶HEAT-AMR (Human-Environment-Animal Transdisciplinary AMR) Research Group, School of Public Health, University of Alberta, Edmonton, Canada
• ⁷Centre for Healthy Communities, School of Public Health, University of Alberta, Edmonton, Canada
• ⁸Canadian Integrated Program for Antimicrobial Resistance Surveillance, Public Health Agency of Canada, Saskatoon, Canada
• ⁹Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, Canada

This study explores the application of nanopore metagenomic sequencing to detect pathogens associated with bovine respiratory disease (BRD) in feedlot cattle, offering a broader and more flexible alternative to conventional diagnostic methods that typically target a limited set of known pathogens. Researchers collected 760 nasal swabs from 240 fall-placed calves (FPC) and120 yearlings (YRL) at arrival and again after 14 days on feed (DOF) from western Canadian commercial feedlots. The sequencing identified 21 distinct viruses from 12 viral families, with multiple viruses frequently detected in individual samples, highlighting the complexity of BRD-associated viral communities. Significant changes in viral prevalence were observed between arrival and 14 DOF, indicating active transmission during early feedlot exposure. In FPC, the prevalence of bovine respiratory syncytial virus (BRSV), bovine parainfluenza virus 3 (BPIV-3), and influenza D virus (IDV) increased significantly over time. In YRL, BRSV, BPIV-3, and bovine viral diarrhea virus type 2 (BVDV-2) were more frequently detected at 14 DOF. Comparative analysis revealed that BRSV and BPIV-3 were more likely to be present in YRL than FPC at arrival, and BPIV-3 and BVDV-2 remained more prevalent in YRL at 14 DOF. These findings suggest risk group-related differences in susceptibility and pathogen exposure. In addition to viruses, the study identified respiratory bacteria and 33 antimicrobial resistance genes (ARGs). In FPC, Mannheimia haemolytica, Histophilus somni, and Pasteurella multocida were the most prevalent bacteria at arrival, with M. haemolytica increasing and P. multocida decreasing by 14 DOF. In YRL, bacterial prevalence remained stable. ARGs were more frequently detected at 14 DOF in both groups, with resistance genes linked to lincosamides, aminoglycosides, and tetracyclines. These findings underscore the dynamic nature of pathogen transmission in feedlots and highlight limitations in current vaccine strategies, particularly for frequently detected viruses like BCoV, BRSV, and BPIV-3. The study demonstrates the value of metagenomic sequencing for simultaneous detection of viruses, bacteria, and ARGs, supporting its potential integration into diagnostic workflows to improve early BRD detection, guide vaccination strategies, and enhance antimicrobial stewardship in cattle production systems.