Shared resistance: the hidden contribution of commensals to pathogen antimicrobial resistance

Antimicrobial resistance (AMR) is usually studied in bacterial pathogens in isolation, overlooking their association with diverse microbial communities that are often dominated by commensals. Commensal bacteria can carry resistance genes and, through horizontal gene transfer (HGT), pass them to pathogens; yet the contribution of these transfers to the emergence and prevalence of pathogen AMR remains largely unquantified. This fellowship integrates evolutionary genomics, experimental assays and mathematical modelling to address this gap. It uses Streptococcus suis, a major cause of disease in pigs and humans, and a common pig tonsil commensal, as a tractable model system to study AMR dynamics across commensal and pathogenic lineages and across scales, from within-host to global. Study of this system will generate a framework for quantifying AMR gene flow that will be applied to other commensal–pathogen systems, allowing us to identify when, and under what conditions, commensals promote pathogen AMR. This research will quantify: (1) how commensals and pathogens differ in gaining, maintaining and spreading AMR; (2) how often, and under what conditions, AMR is transferred between them; and (3) how such transfers influence pathogen AMR. This will reveal the hidden role of commensals in pathogen AMR and inform more effective control strategies.