We hypothesize that antimicrobial exposures increase HGT ARG transfer events from the commensal gut microbiome to enteric pathogens within human hosts, increasing the risk for enteric infections with AMR.


The rapidly rising numbers of infections with pathogenic bacteria resistant to antimicrobials represents a major threat to global health and economic security. To combat this threat, intricate knowledge of the processes underlying the emergence and spread of antimicrobial resistance is necessary.

In this project, we aim to fill an important knowledge gap in antimicrobial resistance research, namely: how do bacterial enteropathogens acquire antimicrobial resistance genes and what are the roles of antibiotic usage and the indigenous human microbiome in this process. The human microbiome is known to be a reservoir for antimicrobial resistance genes (ARGs), but tracking ARGs and their spread among different bacteria has been inherently difficult due to methodological limitations.

AIGHD Research Lead

Vanessa Harris


Amsterdam University Medical Centre (AUMC)

Phase Genomics

Contact info

Project Manager – Mark van Knegsel (




The Netherlands

United States of America