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Department of Genetics


Applied microbial genomics


Microbial genomics, infectious disease, antimicrobial resistance, epidemiology, public health

Research interests 

I study how pathogen genome variation and evolutionary processes impacts their epidemiology and control. I have a particular interest in the dynamics of the accessory genome in bacterial populations, including antimicrobial resistance. Using a combination of microbial genomics, epidemiological approaches, and molecular microbiology, we unpick disease processes at both patient and public health levels in both high income and lower- to middle- income nation settings in collaboration with clinicians, public health practitioners, in vivo experimentalists, and mathematical modellers. I also have an interest in knowledge exchange and policy and have held various external secondments (GO-Science, SEDRIC, and UKHSA.

Key publications

For full details please visit Google Scholar

  • Mason, L.C.E., Greig, D., Cowley, L., Partridge, S., Martinez, E., Blackwell, G., Chong, C., De Silva, M., Bengtsson, R.J., Draper, J., Ginn, A., Sandaradura, I., Sim, E., Iredell, J., Sinchenko, V., Ingle, D., Howden, B., Lefevre, S., Njampkepo, E., Weill, F.X., Ceyssens, P.J., Jenkins, C., Baker, K.S. The evolution and international spread of extensively drug resistant Shigella sonnei (2023) Nature Communications doi: 10.1038/s41467-023-37672-w
  • SEDRIC genomics working group (co-led by Baker K.S.) Harnessing genomics for antimicrobial resistance surveillance (2022) Executive summary
  • De Silva, P.M., Stenhouse, G.E., Blackwell, G.A., Bengtsson, R.J., Jenkins, C., Hall, J.P.J., Baker, K.S. A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success in Shigella.(2022) Proceedings of Royal Society doi: 10.1098/rspb.2022.0581 PMID: 35919999
  • Bengtsson, R.J., Simpkin, A.J., Pulford, C.V., Low, R., Rasko, D.A., Rigden, D.J., Hall, N., Barry, E.H., Tennant, S.M., Baker, K.S. (2022) Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. Nature Microbiology. doi: 10.1038/s41564-021-01054-z

Contact details

Group Leader: Dr Kate Baker


Department of Genetics,
University of Cambridge,
Downing Street,
Cambridge CB2 3EH,
United Kingdom