Professor Stephen Bentley

Professor Stephen Bentley uses high-throughput sequencing to study transmission of bacterial pathogens over time and around the world. He is currently leading a global initiative to assess the impact of pneumococcal vaccination through sequencing 20,000 genomes from isolates collected pre- and post-vaccine implementation.

Stephen completed his PhD and postdoctoral work on the molecular genetics of cell division and virulence gene expression with Professor George Salmond at the Universities of Warwick and Cambridge.

He joined the Sanger Institute in 1998 to work on the annotation and analysis of bacterial genomes. Stephen's early work focused in Streptomyces coelicolor and 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 meningitides showing that gene and genome variation between loci and species was due to common and differing mechanisms of variation. He also found that these variations could confound clinical interventions such as vaccines and antibiotics.

His studies to sequence the capsular biosynthesis genes for all known serotypes of Streptococcus pneumoniae enabled molecular methods for determining serotype. These findings can help to improve the diagnostic and semi-quantitative detection of serotypes in nasopharyngeal samples, providing the information needed to predict the potential for pneumococcal transmission, drug resistance and vaccine evasion.

More recently, Stephen's team has captured the complete genotypic variation of MRSA and pneumococcus to explain epidemiological patterns and phenotypic variation among evolving populations of bacterial pathogens. This work showed the convergent evolution of bacteria in response to the widespread use of various antimicrobial agents and vaccine escape.

Selected Publications

  • Dense genomic sampling identifies highways of pneumococcal recombination.

    Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ, Salter SJ, Harris D, Nosten F, Goldblatt D, Corander J, Parkhill J, Turner P and Bentley SD

    Nature genetics 2014;46;3;305-9

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

    Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP and Lipsitch M

    Nature genetics 2013;45;6;656-63

  • Rapid pneumococcal evolution in response to clinical interventions.

    Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP and Bentley SD

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

  • Evolution of MRSA during hospital transmission and intercontinental spread.

    Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J, Peacock SJ and Bentley SD

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

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

    Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J and Hopwood DA

    Nature 2002;417;6885;141-7

[Wellcome Library, London]

Principal Scientist, Bacterial transmission
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