Professor Stephen D. Bentley | Principal Staff Scientist and Team Leader

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

  • Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition.

    Kwun MJ, Oggioni MR, De Ste Croix M, Bentley SD and Croucher NJ

    Nucleic acids research 2018

  • Effect of vaccination on pneumococci isolated from the nasopharynx of healthy children and the middle ear of children with otitis media in Iceland.

    Quirk SJ, Haraldsson G, Erlendsdóttir H, Hjálmarsdóttir MÁ, van Tonder AJ et al.

    Journal of clinical microbiology 2018

  • Pneumococcal Vaccines: Host Interactions, Population Dynamics, and Design Principles.

    Croucher NJ, Løchen A and Bentley SD

    Annual review of microbiology 2018;72;521-549

  • Bayesian inference of ancestral dates on bacterial phylogenetic trees.

    Didelot X, Croucher NJ, Bentley SD, Harris SR and Wilson DJ

    Nucleic acids research 2018

  • Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae.

    Cleary D, Devine V, Morris D, Osman K, Gladstone R et al.

    Microbial genomics 2018

  • Loss of genomic diversity in a Neisseria meningitidis clone through a colonization bottleneck.

    Lamelas A, Hamid AM, Dangy JP, Hauser J, Jud M et al.

    Genome biology and evolution 2018

  • SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data.

    Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD et al.

    Microbial genomics 2018

  • SuperDCA for genome-wide epistasis analysis.

    Puranen S, Pesonen M, Pensar J, Xu YY, Lees JA et al.

    Microbial genomics 2018

  • The Contribution of Genetic Variation of Streptococcus Pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease.

    Cremers AJH, Mobegi FM, van der Gaast-de Jongh C, van Weert M, van Opzeeland FJ et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018

  • Global distribution of invasive serotype 35D Streptococcus pneumoniae post-PCV13 introduction.

    Lo SW, Gladstone RA, van Tonder AJ, Hawkins PA, Kwambana-Adams B et al.

    Journal of clinical microbiology 2018

  • The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.

    Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R et al.

    PLoS pathogens 2018;14;4;e1006966

  • The effect of environmental and management associated factors on prevalence and diversity ofStreptococcus suisin 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

  • Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

    Lees JA, Kendall M, Parkhill J, Colijn C, Bentley SD and Harris SR

    Wellcome open research 2018;3;33

  • Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.

    van Hal SJ, Steinig EJ, Andersson P, Holden MTG, Harris SR et al.

    Frontiers in microbiology 2018;9;1453

  • Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974.

    Wyres KL, van Tonder A, Lambertsen LM, Hakenbeck R, Parkhill J et al.

    BMC genomics 2013;14;500

Bentley, Stephen D.