The missing element: incorporating mobile genetic elements into risk-based assessment of environmental AMR

Antimicrobial resistance (AMR) is a natural and ancient bacterial defence strategy that has been heavily manipulated by human use of antibiotics. While our understanding of AMR in the environment (microbial habitats outside of human or animal hosts) is rapidly developing, there remains a disconnect between descriptions of the abundance and distribution of AMR determinants in environmental reservoirs and our ability to interpret meaningful risks to health. Here we discuss the missing knowledge that limits our ability to link environmental AMR to a measure of risk, and thus to actionable solutions: (1) an understanding of baseline or ‘natural’ AMR in different environments; (2) the co-occurrence of pathogens with mobile antibiotic resistance genes as an overlooked component of risk; and (3) a comprehensive understanding of the factors that drive selection, persistence and transmission of AMR and resistant pathogens from the environment into other settings. Research focus on these areas will assist our understanding of what components of environmental AMR are relevant, crucial to monitor, and indicative of emerging risk.