Joe's research uses epidemiology, genomics and mathematical transmission modelling to understand how and why people acquire and develop drug-resistant infections in different settings worldwide. He has a focus on a group of bacteria called enterobacterales, which includes common disease causing bacteria like E. coli. Ongoing research includes understanding the transmission routes of resistant enterobacterales in care homes and hospitals in Merseyside, Malawi, and Indonesia, developing genomic and computational methods to define within-person diversity of bacteria at scale to unpick who has transmitted to whom, and understanding the determinants of antimicrobial-resistant infection including socioeconomic factors and how and why infection develops from colonisation.

Joe supervises MSc and PhD student projects on antimicrobial resistance and lectures on clincial management of infection, HIV, and antimicrobial resistance on Diploma in Tropical Medicine and Hygiene and masters programmes.