Dr Joe Lewis

Biography

Joe Lewis is a consultant in infectious diseases whose research aims to tackle the problem of antimicrobial resistance.

He studied natural sciences at Clare College, Cambridge, before postgraduate medicine at St George’s, University of London and clinical postgraduate training in London and Liverpool. He completed his PhD in 2019, a Wellcome clinical PhD fellowship in Blantyre, Malawi. This explored the causes of severe febrile illnesses in adults and the consequences of antimicrobial exposure in driving antimicrobial resistance in sepsis survivors. He was a National Institute for Health and Care Research funded academic clinical lecturer at the University of Liverpool before taking up a role as senior lecturer at Liverpool School of Tropical Medicine in 2024. He combines his research with clinical duties in the NHS.

Research interests

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.

Teaching

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.

Selected research publications

Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults – Journal: Nature Communications – Published: 21st December 2025

Health system drivers of antimicrobial resistance: a qualitative exploration of implications for infection prevention and control in hospitals and long-term care facilities in Merseyside – Journal: Journal of Hospital Infection – Published: 21st October 2025

Colonisation dynamics of extended spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults – Journal: Nature Microbiology – Published: 2nd September 2022

A Longitudinal, Observational Study of Etiology and Long-Term Outcomes of Sepsis in Malawi Revealing the Key Role of Disseminated Tuberculosis – Journal: Clinical Infectious Diseases – Published: 15th May 2022

Aetiology and outcomes of sepsis in adults in sub-Saharan Africa: a systematic review and meta-analysis. – Journal: Critical Care – Published: 11th June 2019

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