Otto, S.

Genomic ASSETS for Livestock: Changing the face of antimicrobial use decisions for livestock
Otto, S.J.G. (presenting author), Trokhymchuk, A., McAllister, T.A., Links, M., Ghosh, K., Stothard, P., Hill J.E., Zaheer, R., Huang, Y., Campbell, J., Erickson, N., Jelinski, N., Fan, X., An, H., Gow. S.P., Adewusi, O., & Waldner, C.W.

Genomic ASSETS (Antimicrobial Stewardship Systems from Evidence-based Treatment Strategies) for Livestock is a revolutionary application of rapid genomic technology to inform antimicrobial use in livestock. Antimicrobial resistance (AMR) is a global threat to public and animal health, placing unprecedented pressure on agriculture to reduce antimicrobial use. Current AMR tests in livestock take 5-7 days. Our diagnostic system will provide results to practicing veterinarians within 24 hours. Bovine Respiratory Disease (BRD) is the most common cause of morbidity/mortality and reason for antimicrobial use in feedlot cattle in western Canada and is a prime target for antimicrobial stewardship. The objective of Genomic ASSETS is to develop a diagnostic system that uses rapid genomic data to inform antimicrobial use decisions for BRD in feedlot cattle at the herd (e.g., pen) level. This abstract presents the program framework and preliminary results.

Phase one*: Develop laboratory and bioinformatics workflows for nanopore sequencing and recombinase polymerase amplification (RPA) application to respiratory swabs from research feedlot cattle. Phase two*: Optimize the pen-level sampling strategies and bioinformatics pipeline so diagnostic data can inform clinical decisions. Phase three*: Epidemiologic analysis to link genomic data to calf health outcomes through dynamic risk assessment model. Phase four*: Field roll-out of the genomic testing strategy to commercial feedlots in Alberta and Saskatchewan. *Phases 1-4 include qualitative studies that engage the beef production chain to inform the design of the diagnostic system. Phase 5: Economic analysis of the system to ensure optimization for the beef feedlot industry.

Preliminary Data have demonstrated that nanopore metagenomic sequencing and RPA will identify bacterial and viral BRD pathogens as well as known resistance genes from respiratory samples.

Genomic ASSETS will change the way we make antimicrobial use decisions for cattle and other livestock by providing rapid, robust diagnostic information to end users.