August 1, 2014

The genomics of Salmonella Paratyphi A, an emergent cause of enteric fever in Asia

Oxford University Clinical Research Unit Vietnam PhD Programme 2014-15

Project 4:

The genomics of Salmonella Paratyphi A, an emergent cause of enteric fever in Asia

Required person: Basic laboratory scientist/bioinformatician/epidemiologist

Type of project: Bacteriology/epidemiology

Potential start date: First quarter 2015

Duration: Four years

Techniques: Epidemiology, bacteriology, bioinformatics, molecular biology

Location: Ho Chi Minh City, Vietnam

Group: Enteric Infections

Supervisor: Stephen Baker

Current status: Ethical approval obtained, funded, publication

Collaborations: Oxford University – UK, Oxford University Clinical Research Unit – Nepal

Brief outline

Salmonella Paratyphi A is a largely understudied cause of enteric fever, and in some locations is replacing Salmonella Typhi as the major cause of bacteremia. Currently there is no data on clinical response to therapy, phylogeny or specific immunological responses. The PhD candidate will perform a retrospective meta-analysis on >1,000 enteric fever cases and investigate the differing clinical features of the various etiological agents. Additionally the student will use bioinformatics to perform sequence analysis on a collection of Salmonella Paratyphi A genome sequences to understand phylogeny and how specific mutations are driving the selection of this important pathogen.

Potential thesis areas

  • The clinical features of Salmonella Paratyphi A infections
  • The population structure of Salmonella Paratyphi A in Kathmandu, Nepal
  • Decreasing susceptibility of Salmonella Paratyphi A to azithromycin
  • The short and long term immunological responses to Salmonella Paratyphi A infections

Associated group publications

Baker S, Holt KE, Clements AC, Karkey A, Arjyal A, Boni MF, Dongol S, Hammond

N, Koirala S, Duy PT, Nga TV, Campbell JI, Dolecek C, Basnyat B, Dougan G, Farrar

JJ. Combined high-resolution genotyping and geospatial analysis reveals modes of

endemic urban typhoid fever transmission. Open Biol. 2011 Oct;1(2):110008. doi:

10.1098/rsob.110008. PubMed PMID: 22645647; PubMed Central PMCID:PMC3352080.

Karkey A, Thompson CN, Nga TVT, Dongol S, Tu LTP, Arjyal A, Phat VV, Martin L, Rondini S, Farrar JJ, Dolecek C, Basnyat B, Baker S. Differential epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: A matched case control investigation in a highly endemic enteric fever setting. PLoS NTD. In press.

PhD-Application-Form

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