Characterising antibiotic-induced collateral damage in the gut microbiome

Antibiotics help clear an ongoing infection, but they can also cause significant collateral damage: they select for drug-resistant strains and cause dysbiosis to the commensal gut microbiota. This antibiotic-induced selection for resistance within the microbiome can facilitate the spread of resistant pathogens to extra-intestinal infections and to other patients (see our recent work: Stracy et al. Science. 2022, 375 (6583), 889-894).

This project will aim to understanding how antibiotics cause collateral damage to the microbiota leading to subsequent resistant infections. This will involve experiments with synthetic and human-derived microbial communities as well as developing microscopy methods to understand the effect of antibiotics on the micro-scale biogeography of the microbiota. The aim is to characterise the key factors that determine how antibiotics affect a patient’s resident microbial population and cause resistant opportunistic pathogens to spread. This will be used to help develop new ways to minimize the spread of antibiotic resistance both within and between patients. The project would suit applicants with a strong background in microbiology and keen interest in developing new ways to combat antibiotic resistance.