Dr Joe Lewis

Senior Lecturer in Infectious Diseases

Joe is a consultant in Infectious Diseases whose research uses techniques like mathematical modelling and genomics 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 postrgraduate 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 inllness in adults and the consequences of antimicrobial exposure in driving antimicrobial resistance in sepsis survivors. He took up a role as senior lecturer at LSTM in 2024, and combines his research with clinical duties in the NHS.

Ongoing research includes understanding the transmission routes of resistant Enterobacterales bacteria in a variety of settings including in Merseyside, Malawi, and Indonesia; developing genomic and computational methods to define within-person diversity of bacteria at scale, and to use these data to inform transmission modelling; and understanding the determinants of antimicrobial-resistant infection including socioeconomic factors.

Selected publications

  • Lewis JM, Mphasa M, Banda R, Beale MA, Mallewa J, Anscome C, Zuza A, Roberts AP, Heinz E, Thomson NR, Feasey NA. Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity. Microb Genom. 2023;9(6):mgen001035. doi: 10.1099/mgen.0.001035.

    Lewis JM, Mphasa M, Banda R, Beale MA, Heinz E, Mallewa J, Jewell C, Faragher B, Thomson NR, Feasey NA. Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults. Nat Microbiol. 2022;7(10):1593-1604. doi: 10.1038/s41564-022-01216-7.

    Lewis JM, Mphasa M, Banda R, Beale MA, Mallewa J, Heinz E, Thomson NR, Feasey NA. Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi. Microb Genom. 2022;8(3):000778. doi: 10.1099/mgen.0.000778.

    Lewis JM, Mphasa M, Keyala L, Banda R, Smith EL, Duggan J, Brooks T, Catton M, Mallewa J, Katha G, Gordon SB, Faragher B, Gordon MA, Rylance J, Feasey NA. A Longitudinal, Observational Study of Etiology and Long-Term Outcomes of Sepsis in Malawi Revealing the Key Role of Disseminated Tuberculosis. Clin Infect Dis. 2022;74(10):1840-1849. doi: 10.1093/cid/ciab710. PMID: 34407175; PMCID: PMC9155594.

    Barr DA†, Lewis JM†, Feasey N, Schutz C, Kerkhoff AD, Jacob ST, Andrews B, Kelly P, Lakhi S, Muchemwa L, Bacha HA, Hadad DJ, Bedell R, van Lettow M, Zachariah R, Crump JA, Alland D, Corbett EL, Gopinath K, Singh S, Griesel R, Maartens G, Mendelson M, Ward AM, Parry CM, Talbot EA, Munseri P, Dorman SE, Martinson N, Shah M, Cain K, Heilig CM, Varma JK, von Gottberg A, Sacks L, Wilson D, Squire SB, Lalloo DG, Davies G, Meintjes G. Mycobacterium tuberculosis bloodstream infection prevalence, diagnosis, and mortality risk in seriously ill adults with HIV: a systematic review and meta-analysis of individual patient data. Lancet Infect Dis. 2020;20(6):742-752. doi: 10.1016/S1473-3099(19)30695-4.
    † = Joint first authorship

    Lewis JM, Feasey NA, Rylance J. Aetiology and outcomes of sepsis in adults in sub-Saharan Africa: a systematic review and meta-analysis. Crit Care. 2019 11;23(1):212. doi: 10.1186/s13054-019-2501-y.