Exploiting genomics to mitigate the public health impact of antimicrobial resistance

Antimicrobial resistance (AMR) is a major global public health threat, which has been largely driven by the excessive use of antimicrobials. Control measures are urgently needed to slow the trajectory of AMR but are hampered by an incomplete understanding of the interplay between pathogens, AMR encoding genes, and mobile genetic elements at a microbial level. These factors, combined with the human, animal, and environmental interactions that underlie AMR dissemination at a population level, make for a highly complex landscape. Whole-genome sequencing (WGS) and, more recently, metagenomic analyses have greatly enhanced our understanding of these processes, and these approaches are informing mitigation strategies for how we better understand and control AMR. This review explores how WGS techniques have advanced global, national, and local AMR surveillance, and how this improved understanding is being applied to inform solutions, such as novel diagnostic methods that allow antimicrobial use to be optimised and vaccination strategies for better controlling AMR. We highlight some future opportunities for AMR control informed by genomic sequencing, along with the remaining challenges that must be overcome to fully realise the potential of WGS approaches for international AMR control.

Automated summary

Antimicrobial resistance (AMR) is a significant global public health threat caused by excessive use of antimicrobials. The interplay between pathogens, AMR encoding genes, and mobile genetic elements on a microbial level is not fully understood, hampering control measures. Whole-genome sequencing (WGS) and metagenomic analyses have improved our understanding of these processes, informing mitigation strategies and novel diagnostic methods to optimize antimicrobial use and control AMR. Future opportunities for AMR control are identified, alongside challenges that need to be addressed to fully utilize WGS approaches for international AMR control.