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An Interdisciplinary Research Centre at the University of Cambridge


I am a Group Leader at the Institute and a Food Standards Agency Fellow, where my interests are the epidemiology, evolution and dynamics of foodborne and zoonotic bacteria, with a particular focus on antimicrobial resistance (AMR). I was awarded a BSc in biomedical toxicology and an MSc in epidemiology from the University of Guelph, followed by a PhD at the University of Glasgow, where I took an epidemiological and ecological approach to the study of AMR in E. coli, and in Salmonella from animals and humans.

After moving to the Wellcome Trust Sanger Institute, my work utilised whole genome sequencing (WGS) to examine, in the greatest resolution, the evolution and transmission of both bacteria and AMR between and within different host populations. This lead to important insights into the dynamics in Scotland of a globally distributed Salmonella epidemic, demonstrating that there were distinguishable bacterial populations in animals and humans. I have also applied these phylogenetic and comparative genomics techniques to other bacteria, including ShigellaCampylobacter, and Vibrio cholerae.

I was awarded a BBSRC Anniversary Future Leader fellowship at the University of Cambridge in 2015, where I used short and long-read sequencing to investigate the dynamics of AMR and cross-species transmission in Salmonella in Vietnam. I have also become very interested in the role of commensal bacteria as reservoirs of AMR genes, and used metagenome sequencing to try to quantify their contribution to the AMR burden of pathogens. In 2017 I moved to the Quadram Institute, where my group studies the epidemiology, evolution and AMR of pathogenic and commensal bacteria throughout the food chain.


Key publications: 

Hunt, M.H., Mather, A.E., Sánchez-Busó, L., Page, A.J., Parkhill, J., Keane, J.A. and Harris, S.R. (2017) ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb. Gen.

Petrovska, L., Mather, A.E., AbuOun, M., Branchu, P., Harris, S.R., Connor, T., Hopkins, K.L., Underwood, A., Lettini, A.A., Page, A., Bagnall, M., Wain, J., Parkhill, J., Dougan, G., Davies, R. and Kingsley, R.A. (2016) Microevolution of monophasic Salmonella Typhimurium during epidemic, United Kingdom, 2005-2010. Emerg. Inf. Dis. 22. 617-624.

Mather, A.E., Vaughan, T.G. and French, N.F. (2015) Molecular approaches to understanding transmission and source attribution in non-typhoidal Salmonella and their application in Africa. Clin, Infect. Dis. 61 Suppl 4, S259-65.

Mather, A.E., Reid, S.W.J., Maskell, D.J., Parkhill, J., Fookes, M.C., Harris, S.R., Brown, D.J., Coia, J.E., Mulvey, M.R., Gilmour, M.W., Petrovska, L., de Pinna, E., Kuroda, M., Akiba, M., Izumiya, H., Connor, T.R., Suchard, M.A., Lemey, P., Mellor, D.J., Haydon, D.T. and Thomson, N.R. (2013) Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science. 341. 1514-1517.

Mather, A.E., Matthews, L., Mellor, D.J., Reeve, R., Denwood, M.J., Boerlin, P., Reid-Smith, R.J., Brown, D.J., Coia, J.E., Browning, L.M., Haydon, D.T., and Reid, S.W.J. (2012) An ecological approach to assessing the epidemiology of antimicrobial resistance in animal and human populations. Proc. R. Soc. B. 279, 1630 – 1639.

Group Leader at Quadram Institute
Epidemiology, evolution and dynamics of foodborne and zoonotic bacteria, with a particular focus on antimicrobial resistance (AMR)
Dr Alison   Mather
Not available for consultancy


Person keywords: 
Antimicrobial resistance