Genomic ASSETS (Antimicrobial Stewardship Systems from Evidence-based Treatment Strategies) for Livestock

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 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.This project has provided: 1) Genomic lab methods for processing large numbers of clinical samples that can be implemented by a commercial, diagnostic laboratory for use in feedlot production; 2) Large-scale, automated, and searchable bioinformatics and data management systems to process sequencing data from large numbers of samples; 3) 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; 4) The evaluation of diagnostic evidence from the application and interpretation of genomic tools to inform recommendations for prudent antimicrobial use; and 5) a management framework for application of long-read metagenomics in BRD management in commercial feedlots.Our genomics-based precision health strategy will support Canada's beef and livestock industry to: 1) Comply with WHO guidelines that could result in AMR trade restrictions and ensure a competitive advantage for Canadian beef; 2) Inform AMU and improve animal health; and 3) Support AMU stewardship goals for BRD management; 4) Guide vaccination for viral BRD pathogens.To combat the global challenge of antimicrobial resistance (AMR) and 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 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.This project has provided: 1) Genomic lab methods for processing large numbers of clinical samples that can be implemented by a commercial, diagnostic laboratory for use in feedlot production; 2) Large-scale, automated, and searchable bioinformatics and data management systems to process sequencing data from large numbers of samples; 3) 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; 4) The evaluation of diagnostic evidence from the application and interpretation of genomic tools to inform recommendations for prudent antimicrobial use; and 5) a management framework for application of long-read metagenomics in BRD management in commercial feedlots.Our genomics-based precision health strategy will support Canada's beef and livestock industry to: 1) Comply with WHO guidelines that could result in AMR trade restrictions and ensure a competitive advantage for Canadian beef; 2) Inform AMU and improve animal health; and 3) Support AMU stewardship goals for BRD management; 4) Guide vaccination for viral BRD pathogens.