Honorary Faculty - Stephen Baker

Stephen has been associated with the Sanger Institute since 1998, where he started as a pathogen genome finisher, and he has worked closely with the Institute ever since. Stephen’s research focuses on enteric and zoonotic pathogens, focussing mainly on bacteria and viruses.

Stephen has been based at the Wellcome Trust Major Overseas Programme in Ho Chi Minh City Vietnam since 2007 and is Head of the Enteric Infections group. Before joining the Programme, he was a postdoctoral training fellow at the Wellcome Trust Sanger Institute for two years. This pivotal period of postdoctoral training allowed him to understand the applications of genome sequencing for epidemiology and he performed some early work on the evolution and emergence of Salmonella Typhi, the causative agent of typhoid fever.

His work in Vietnam has extended his knowledge of pathogen diversity and evolution. Since his appointment at the University of Oxford he has developed as an independent scientist and is establishing himself in the field of enteric infections (bacteria and viruses) and is building an international research team. Stephen holds concurrent appointments as a research lecturer at the University of Oxford and as a senior lecturer at the London School of Hygiene of Tropical Medicine. He also holds the prestigious Royal Society / Wellcome Trust Sir Henry Dale Fellowship, investigating the phylogeography of Shigella infections in Ho Chi Minh City and he is principal investigator on a Wellcome Trust-funded strategic award entitled the Wellcome Trust - Vietnam Initiative on Zoonotic InfectiONS (VIZIONS).

Selected Publications

  • Tracking the establishment of local endemic populations of an emergent enteric pathogen.

    Holt KE, Thieu Nga TV, Thanh DP, Vinh H, Kim DW, Vu Tra MP, Campbell JI, Hoang NV, Vinh NT, Minh PV, Thuy CT, Nga TT, Thompson C, Dung TT, Nhu NT, Vinh PV, Tuyet PT, Phuc HL, Lien NT, Phu BD, Ai NT, Tien NM, Dong N, Parry CM, Hien TT, Farrar JJ, Parkhill J, Dougan G, Thomson NR and Baker S

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;43;17522-7

  • Endemic norovirus infections in children, Ho Chi Minh City, Vietnam, 2009-2010.

    My PV, Thompson C, Phuc HL, Tuyet PT, Vinh H, Hoang NV, Minh PV, Vinh NT, Thuy CT, Nga TT, Hau NT, Campbell J, Chinh NT, Thuong TC, Tuan HM, Farrar J and Baker S

    Emerging infectious diseases 2013;19;6;977-80

  • Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure.

    Baker S, Duy PT, Nga TV, Dung TT, Phat VV, Chau TT, Turner AK, Farrar J and Boni MF

    eLife 2013;2;e01229

  • Identification of immunogenic Salmonella enterica serotype Typhi antigens expressed in chronic biliary carriers of S. Typhi in Kathmandu, Nepal.

    Charles RC, Sultana T, Alam MM, Yu Y, Wu-Freeman Y, Bufano MK, Rollins SM, Tsai L, Harris JB, LaRocque RC, Leung DT, Brooks WA, Nga TV, Dongol S, Basnyat B, Calderwood SB, Farrar J, Khanam F, Gunn JS, Qadri F, Baker S and Ryan ET

    PLoS neglected tropical diseases 2013;7;8;e2335

  • Immune profiling with a Salmonella Typhi antigen microarray identifies new diagnostic biomarkers of human typhoid.

    Liang L, Juarez S, Nga TV, Dunstan S, Nakajima-Sasaki R, Davies DH, McSorley S, Baker S and Felgner PL

    Scientific reports 2013;3;1043

* quick link - http://q.sanger.ac.uk/67ykyvud