Antimicrobial resistance (AMR) is a global threat to animal and human health, food security, economic growth, and development that is already killing worldwide 1.3 million people annually. It is increasingly recognized that a One Health approach is required to mount an effective response to the AMR crisis, which necessitates monitoring the spread and impact of AMR across sectors. Current AMR surveillance approaches are largely based on isolation of specific bacterial species; these approaches are limited because they are onerous and time consuming, and incapable of detecting dissemination mediated by non-pathogenic species.
We propose to expand surveillance capabilities using a sensitive long-read amplicon sequencing of antimicrobial resistance genes (ARGs), which will produce data that could be tabulated for surveillance across One Health reservoirs and for comparison with knowledge in public sequence databases. The amplicon sequencing approach will be complemented by hybridization capture panels of ARGs to reveal their genomic contexts (i.e., flanking regions). To ensure the relevance for policy makers, the development of these metagenomic solutions will be achieved in conjunction with public health modelers expanding an integrated assessment model designed to holistically assess AMR threats. The incorporation of metagenomic data to this model will allow the assessment of new pathways of dissemination, and the refinement or adjustment of the model structure to account for a better understanding of the connections between sectors.