Professor Stephen D. Bentley | Principal Staff Scientist

Bentley, Stephen D.

Using bacterial pathogen genomics to understand patterns of colonisation, transmission and genetic associations with disease. Focus on pathogens associated with respiratory infection and particulalry those which have a major disease burden in resource-poor settings.

Stephen joined the Sanger Institute in 1998 to work on the annotation and analysis of bacterial genomes. His early work focused on the antibiotic-producing soil bacterium Streptomyces coelicolor and the rare human pathogen Tropheryma whipplei and provided insights into the mechanisms of horizontal gene transfer, generation of antigenic variation and the prevalence of antibiotic production genes. This was followed by research into Streptococcus pneumoniae and Neisseria meningitidis showing that gene and genome variation between loci and species was due to common and differing mechanisms of variation. The study to sequence the capsular biosynthesis genes for all known serotypes of S. pneumoniae enabled molecular methods for determining serotype which have brought important new understnading of pneumococcal colonisaion and transmission.

Since the development of high throughput sequencing Stephen's research has focused on population genomics with pioneering papers on MRSA (2010) and the pneumococcus (2011) revealing patterns of international spread, vaccine escape and the aquisition of antimicrobial resistance.


  • Evolution of MRSA during hospital transmission and intercontinental spread.

    Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK et al.

    Science (New York, N.Y.) 2010;327;5964;469-74

  • Rapid pneumococcal evolution in response to clinical interventions.

    Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J et al.

    Science (New York, N.Y.) 2011;331;6016;430-4

  • Dense genomic sampling identifies highways of pneumococcal recombination.

    Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P et al.

    Nature genetics 2014;46;3;305-309

  • Population genomics of post-vaccine changes in pneumococcal epidemiology.

    Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM et al.

    Nature genetics 2013;45;6;656-63

  • Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.

    Harris SR, Cartwright EJ, Török ME, Holden MT, Brown NM et al.

    The Lancet. Infectious diseases 2013;13;2;130-6

  • Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes.

    Bentley SD, Aanensen DM, Mavroidi A, Saunders D, Rabbinowitsch E et al.

    PLoS genetics 2006;2;3;e31

  • Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).

    Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR et al.

    Nature 2002;417;6885;141-7

  • The effect of environmental and management associated factors on prevalence and diversity of<i>Streptococcus suis</i>in clinically healthy pig herds of China and UK.

    Zou G, Zhou J, Xiao R, Zhang L, Cheng Y et al.

    Applied and environmental microbiology 2018

Bentley, Stephen D.