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Developing GWAS approaches to decipher the drivers of Bordetella pertussis adaptation during re-emergence

  • Full or part time
  • Application Deadline
    Sunday, January 12, 2020
  • Awaiting Funding Decision/Possible External Funding
    Awaiting Funding Decision/Possible External Funding

Project Description

Genome rearrangement, the reordering of genes along the chromosome, is widespread among bacteria. It is thought to affect bacterial phenotype (behaviour) and contribute to their evolution and adaptation. However, the difficulty of isolating the effect of genome arrangement from other genetic variation means studies in this important area are lacking.

The bacterium Bordetella pertussis causes whooping cough, an important respiratory tract disease that during the last decade has been steadily increasing in incidence in the UK and other countries. Pertussis is an area of high concern within PHE due to this resurgence. B. pertussis offers a unique model to study the role of genome rearrangement in adaptation as it exhibits extensive rearrangement among strains but very low levels of other genetic variation. Genome-wide association studies (GWAS) are a cornerstone of genetics that identify associations between specific genetic variations and specific traits; but they currently focus on gene content and simple DNA-sequence level variations.

In this Ph.D. project GWAS approaches will be developed to study the effect of genome arrangement on B. pertussis phenotype, creating fundamental new understanding of B. pertussis evolution and adaptation that is contributing to pertussis resurgence. The project will involve training in bioinformatics, molecular microbiology and immunoassays, applied to understanding the resurgence of this important pathogen. The combination of bioinformatics and wet lab studies creates a multidisciplinary project, with cutting edge training in pathogen genomics.

Primarily based in the Preston group in the Department of Biology and Biochemistry at Bath, the project will be conducted collaboratively with Prof. Gorringe at Public Health England at Porton Down. This provides an excellent opportunity to receive specialist training in the labs at Porton and to learn about the role of this executive agency of the Department of Health in public health research and policy. The student will conduct a placement at PHE Porton as part of their project studies and will also have access to wider training opportunities within the PHE.

Candidate requirements:

Applicants should hold, or expect to receive, a First Class or high Upper Second Class UK Honours degree (or the equivalent qualification gained outside the UK) in a relevant subject. A master’s level qualification would also be advantageous. Non-UK applicants must meet our English language entry requirement http://www.bath.ac.uk/study/pg/apply/english-language/index.html.

How to apply:

Informal enquiries are welcomed and should be addressed to Dr Andrew Preston.

Formal applications should be made via the University of Bath’s online application form:

Please ensure that you quote the supervisor’s name and project title in the ‘Your research interests’ section.

More information about applying for a PhD at Bath may be found here:

Anticipated start date: 28 September 2020.

Funding Notes

It is anticipated that funding will be secured for a 3.5-year University Studentship in collaboration with Public Health England. The studentship will cover UK/EU tuition fees, a stipend at the UKRI Doctoral Stipend rate (£15,009 per annum, 2019-20 rate) and an allowance for research and training expenses. This advertisement will be updated when confirmation of funding has been received. Interested candidates are invited to contact the lead supervisor for more information.

We also welcome year-round applications from applicants who can fund their own studies or secure their own external funding.


Brookes, C., et al., Bordetella pertussis isolates vary in their interactions with human complement components. Emerg Microbes Infect, 2018. 7: 81.

Ring, N., et al., Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing. Microbial Genomics, 2018. 4: 10.1099/mgen.0.000234.

Weigand, M.R., et al., The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement. Journal of Bacteriology, 2017. 199: e00806-16.

How good is research at University of Bath in Biological Sciences?

FTE Category A staff submitted: 24.50

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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