Background

SEARCHER (Surveillance for Emerging Antimicrobial Resistance through Characterization of the uncharted Environmental Resistome) is a research project supported by JPIAMR.

A major issue in curbing AMR is that we rarely know which newly emerged forms of AMR may become significant threats to human health until antibiotic resistance genes (ARGs) are already widespread in pathogenic bacteria. Therefore, it is difficult to employ surveillance to preventively identify emerging risks. SEARCHER seeks to characterize emergent ARGs in the environment, allowing their inclusion into AMR surveillance and detection before they become clinical problems. This will result in an early warning system for emerging AMR threats.

SEARCHER's Plan to Tackle AMR

• Identify novel ARGs using functional metagenomics, shotgun metagenomic sequencing, and exposure experiments enriching relevant ARGs

• Develop computational methods to determine the mobility of novel ARGs and their potential for transfer to pathogens

• Pinpoint specific early warning indicators for emerging ARGs using computational, artificial intelligence-based approaches

• Improve monitoring protocols for AMR so that they can be quickly updated with novel ARGs

• Define important settings where humans interact with environmental bacteria carrying novel ARGs

• Sample locations at the interface of humans, animals and the environment using state-of-the-art approaches such as long-read and functional metagenomics

• Provide resources for the integration of emerging ARGs into routine AMR surveillance

The Big Data Biology Lab's Role

Dr. Luis Pedro Coelho is a research project partner with SEARCHER. He received a $510,187.65 grant from the National Health and Medical Research Council in Australia as part of JPIAMR.

Our work on SEARCHER builds on the EMBARK project, which is an international collaboration that aims to establish the baseline status of antimicrobial resistance in the environment, and the GMGC where we catalogue all the genomic diversity available in publicly-available databases.

The project will employ a postdoctoral researcher and a graduate student and work with groups in Sweden, Germany, France, Pakistan, and Nigeria.