An omics-based framework for assessing the health risk of antimicrobial resistance genes

Abstract Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that high-risk. Here, we developed an ‘omics-based’ framework evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our classifies human-associated, mobile (3.6% ARGs) as highest risk, which further differentiate ‘current threats’ (Rank I; 3%) - already present pathogens ‘future II; 0.6%) novel emerging from non-pathogens. identified 73 threat’ families. Of these, 35 were 37 high-risk proposed by World Health Organization other literature; remaining 38 significantly enriched in hospital plasmids. By evaluating pathogen genomes released since construction, confirmed recently transferred into Rank II (‘future threats’). Lastly, applied gut microbiome fecal microbiota transplantation donors. We found although (73% genomes), only 8.9% contained ARGs. provides easy-to-implement approach identify current future antimicrobial threats, with potential clinical applications including reducing microbiome-based interventions.