OMIC approach to AMR mitigation

Funding period: 2024-2027
Lead: Rhiannon Wallace
Total GRDI funding: $1,244,453

In Canada, approximately 15 people per day lost their life to antimicrobial-resistant (AMR) infections in 2018. The increased proximity of livestock operations to communities poses a public health risk as livestock are reservoirs for zoonotic pathogens and AMR bacteria (ARB). Dairy farms in peri-urban settings, such as the Fraser Valley, are potential hotspots for transmission of AMR between humans, animals and the environment. Our preliminary findings, in collaboration with other GoC departments, through GRDI-AMR2 has shown along the One-Health Continuum Enterococcus spp. and E. coli harboring resistance determinants of significance to public health are highly prevalent in dairy production systems and surrounding environments. Our current research is generating critically important baseline data, while this study will focus on pathogen detection and mitigating AMR transmission. This innovative research will assess the suitability of the MinION sequencer for rapid detection of pathogens and AMR determinants in food and environmental samples. Enterococcus spp., such as E. faecium, is an emerging pathogen with a remarkable ability to evolve and transmit resistance determinants, particularly to other bacteria which pose considerable risk to human and animal health. Presently, limited work has been done to characterize the resistome of Enterococcus spp. isolated from non-clinical sources. Isolates that are presently being collected seasonally in British Columbia (GRDI-AMR2) will be sequenced to characterize their resistome and mobile genetic elements in order to identify new genomic targets for phage-based plasmids to control AMR pathogens. This innovative biovigilance tool for pathogen detection, which relies on metagenomics, and our novel biological approach to controlling AMR will be applicable to multiple sectors and commodities.