Surveillance for Emerging Antimicrobial Resistance through Characterization of the uncharted Environmental Resistome

Research Project, 2023 – 2026

Antimicrobial resistance (AMR) is a major healthcare challenge that, unless controlled, will cause millions of deaths annually in just a couple of decades. A major issue in curbing AMR is that we seldom know what newly emerged antibiotic resistance genes (ARGs) to look for until they are already widespread in pathogenic bacteria. This makes it impossible to use surveillance to preventively identify risks for emergence of new ARGs. In this project, we will characterize emergent ARGs in the environment, allowing their inclusion into AMR surveillance and detection in risk environments before they become clinical problems. To achieve this, we will:
1) Identify novel ARGs using functional metagenomics, shotgun metagenomic sequencing and exposure experiments
2) Investigate the mobility of novel ARGs and their potential for transfer to pathogens
3) Pinpoint specific early warning indicators for emerging ARGs
4) Improve monitoring protocols for AMR so that they can be quickly updated with novel ARGs
5) Define important settings where humans interact with resistant environmental bacteria by sampling the interface of humans, animals and the environment
6) Provide resources for the integration of emerging ARGs in routine AMR surveillance

The project will result in an early warning system for emerging AMR threats. The system will be implementable in real-world surveillance in human, animal and environmental settings targeting applicability, affordability, and high information content.