Profiling the gut resistome to unlock antimicrobial resistance biology and inform clinical risk.

Abstract

Antimicrobial resistance (AMR) is a global crisis, amplified by slow antibiotic development, inadequate surveillance, and limited understanding of resistance gene dissemination. Traditional detection methodologies fail to capture the complexity and interconnectivity of AMR, highlighting the need for novel approaches. Gut resistome profiling using next-generation sequencing enables untargeted detection of AMR genes within microbial communities, revealing their acquisition, transfer and persistence while providing early warning signals for emerging resistance. This review synthesises advances in resistome science, highlights translational opportunities for infection risk prediction and surveillance, and identifies future directions for integrating gut resistome profiling into precision public health and stewardship frameworks.