Why is this research important to Alberta?

• To combat the global challenge of antimicrobial resistance (AMR) and the need for antimicrobial stewardship, animal healthcare providers require access to timely laboratory diagnostic information that supports prudent antimicrobial selection.
• The overall aim of this project was to develop and pilot practical testing strategies for livestock management systems to enable large-scale application of leading-edge genomic technologies by the livestock industry.
• High-risk calves entering feedlots are routinely treated with antimicrobials for bovine respiratory disease (BRD), which contributes to selective pressure for AMR.
• Calves are managed as groups in feedlot pens and BRD circulates much as colds and flu circulate in classrooms of children.
• Our genomics-based testing provides necessary data to better inform pen- and feedlot-level antimicrobial treatment strategies for BRD in Canadian feedlot cattle.

What is the goal of this work? How will genomics be used?

This project has provided:

• genomic lab methods for processing large numbers of clinical samples that can be implemented by a commercial, diagnostic laboratory for use in feedlot production;
• large-scale, automated, and queryable bioinformatics and data management systems to process sequencing data from large numbers of samples;
• precision sampling and testing strategies to identify BRD pathogens and AMR status for pens of calves in feedlots that have been applied in a research feedlot as well as commercial feedlots;
• the evaluation of diagnostic evidence from the application and interpretation of genomic tools to inform recommendations for prudent antimicrobial use; and
• a management framework for the application of long-read metagenomics in BRD management in commercial feedlots.

The project team included researchers from the University of Saskatchewan, University of Alberta and Agriculture and Agri-Food Canada.

Researchers partnered with regional labs, private veterinary clinics, Beef Cattle Research Council (BCRC), Natural Sciences and Engineering Research Council of Canada (NSERC), Alberta Beef Producers (ABP), Saskatchewan Cattle Association (SCA), Agriculture Development Fund (ADF) and Public Health Agency of Canada (PHAC).

What are the expected benefits, and how will the research findings be shared?

• The Canadian beef industry contributes $29 billion annually to GDP, with western feedlots finishing 79% of slaughter cattle.
• Over 90% of injectable antimicrobial use in feedlot cattle targets bovine respiratory disease (BRD).
• Pen- and feedlot-level laboratory data on BRD pathogens and antimicrobial resistance provide timely support for stewardship.
• Project findings could reduce risks of future trade restrictions under Codex AMR guidelines that may threaten Canada’s $5.02 billion beef export market.
• This genomics-based precision health strategy will help the industry comply with WHO guidance, inform antimicrobial use, improve animal health, support BRD stewardship, and guide vaccination against viral BRD pathogens nationally.

Related Resources

Related information can be accessed through:

• News article: $5.6M grant to improve the use of antibiotics in food animals | Public Health
• Research publication: Diagnostic sensitivity and specificity of metagenomic sequencing and qPCR for detection of viruses associated with bovine respiratory disease estimated using Bayesian latent class models
• Research publication: Respiratory Bacteria and Antimicrobial Resistance Genes Detected by Long-Read Metagenomic Sequencing Following Feedlot Arrival, Subsequent Treatment Risk and Phenotypic Resistance in Feedlot Calves
• Research publication: Comparison of Short Nasal Swab and Deep Nasopharyngeal Swab Sampling Methods to Describe BRD-Associated Viruses and Bacteria Detected Using a Metagenomics Approach Optimized for Virus Recovery in Fall-Placed Beef Calves Shortly after Feedlot Arrival
• Research publication: Opportunities for Laboratory Testing to Inform Antimicrobial Use for Bovine Respiratory Disease: Application of Information Quality Value Stream Maps in Commercial Feedlots
• Research publication: Laboratory testing to inform antimicrobial use for bovine respiratory disease: Perceptions of Canadian feedlot veterinarians