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Cambridge Infectious Diseases

An Interdisciplinary Research Centre at the University of Cambridge

Studying at Cambridge


Professor Stephen Bentley

Professor Stephen Bentley

Wellcome Sanger Institute

Genomics of bacterial pathogenesis with a particular focus on pneumonia and meningitis

Stephen Bentley is accepting applications for PhD students.

Stephen Bentley is available for consultancy.


Senior Research Associate/Principal Scientist

Genomics of Bacterial Pathogenesis

Stephen Bentley has a joint position between the Department of Medicine and the Wellcome Trust Sanger Institute. His expertise is in the genomics of bacterial pathogenesis with a particular focus on pneumonia and meningitis. Stephen pioneered the use of high throughput genomics to improve understanding of fundamental processes of bacterial evolution such as point mutation rate and homologous recombination. This approach has been successfully applied to study the phenomenon of vaccine escape in the pneumococcus, the main cause of vaccine preventable pneumonia mortality worldwide. He is also applying genomics to study local population dynamics, person-to-person transmission, global spread and micro-evolution during infection. Stephen’s work is greatly empowered by strong collaborative links with clinicians and scientist worldwide, many based in countries where infectious disease burden is high.

Research themes

Pathogen Biology and Evolution:
Bacterial Pathogens:

Bacterial genomics and evolution

Connections in Africa:
  • MRC Gambia, The Gambia
  • MLW, Blantyre, Malawi
  • National Institute for Communicable Diseases, Johannesburg, South Africa


Connections in Asia:
  • SMRU, Mae Sot, Thailand
  • Mahidol University, Bangkok, Thailand
  • Angkor Hospital for Children, Siem Reap, Cambodia
Connections in South America:
  • Hospital de Niños Roberto del Río.
  • Santiago, Chile
Connections in North America:
  • Harvard University, USA
  • Emory University, USA
  • Rockefeller University, USA
  • CDC, Atlanta, USA
Connections in Europe:
Connections in Australasia:
  • University of Sydney, Australia

Departments and Institutes

Senior Research Associate
Wellcome Sanger Institute:
Principal Scientist
Centre for Pathogen Evolution:
Consortium Members and Partners:


  • Genomics
  • Evolution
  • Sequencing
  • Immune Evasion
  • Molecular Biology
  • Drug Resistance
  • Epidemiology
  • Host-Pathogen Interaction
  • Molecular epidemiology
  • Public Health
  • Pathogen Evolution
  • Infection
  • Developing World
  • Pathogenesis
  • Otitis media
  • Bioinformatics
  • Bacteriology


  • Genomics
  • Meningitis
  • MRSA
  • Staphylococcus aureus
  • Streptococcus
  • Streptococcus pneumoniae
  • Tuberculosis

Key Publications

Harris, S.R.; Cartwright, E.J.P.; Török, M.E.; Holden, M.T.G.; Brown, N.M.; Ogilvy-Stuart, A.L.; Ellington, M.J.; Quail, M.A.; Bentley, S.D.; Parkhill, J.; Peacock, S.J. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. The Lancet Infectious Diseases 2012 Nov 13.

Croucher, N.J.; Harris, S.R.; Fraser, C.; Quail, M.A.; Burton, J.; van der Linden, M.; McGee, L.; von Gottberg, A.; Song, J.H.; Ko, K.S.; Pichon, B.; Baker, S.; Parry, C.M.; Lambertsen, L.M.; Shahinas, D.; Pillai, D.R.; Mitchell, T.J.; Dougan, G.; Tomasz, A.; Klugman, K.P.; Parkhill, J.; Hanage, W.P.; Bentley, S.D. Rapid pneumococcal evolution in response to clinical interventions. Science. 2011b Jan 28;331(6016):430-434.

Harris, S.R.; Feil, E.J.; Holden, M.T.; Quail, M.A.; Nickerson, E.K.; Chantratita, N.; Gardete, S.; Tavares, A.; Day, N.; Lindsay, J.A.; Edgeworth, J.D.; de Lencastre, H.; Parkhill, J.; Peacock, S.J.; Bentley, S.D. Evolution of MRSA during hospital transmission and intercontinental spread. Science. 2010 Jan 22;327(5964):469-474.