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Understanding the impact of vaccination on the spread of antibiotic resistance using phylogenetics

   College of Medicine and Veterinary Medicine

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  Dr K Atkins, Prof Stefan Flasche, Dr S Lycett  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

Vaccines against bacterial pathogens have been proposed as a means to combat antibiotic resistant infections (e.g. Lipsitch and Siber, 2016; Atkins et al. 2018). For example, by reducing the total burden of pneumococcal infections, pneumococcal conjugate vaccines would also reduce the number of resistant pneumococcal infections. However, the exact impact of these vaccines are determined by the epidemiological and evolutionary dynamics of the circulating pathogens (Davies et al., 2021). Specifically, while the spatial structure of antibiotic use, the pathogen diversity and the within-host dynamics of infection can all determine the frequency of antibiotic resistant infections, the relative importance of these mechanisms is unknown. Therefore, understanding the impact of vaccines to prevent antibiotic resistance hinges on quantifying these dynamics.

Phylogenetic analysis provides a tool to quantify infectious disease dynamics by leveraging the information contained in genetic sequence data to infer epidemic spread. This project will use rich genetic and complementary epidemiological data from a multi-year cluster randomized trial for a pneumococcal conjugate vaccine (PCV) in Vietnam to help elucidate the underlying dynamics of S. pneumoniae, a major cause of childhood pneumonia. Using deep sequence genetic data across four years of sampling in a high antibiotic use setting, these data will provide unparalleled insight into the dynamics of drug resistance and the impact of pneumococcal conjugate vaccines on drug resistant infections.

The project will use an interdisciplinary combination of genetic sequence data analysis, epidemiology, and phylogenetic analysis. The candidate will develop their quantitative skills using phylogenetic, statistical and mathematical analysis. The student will develop or extend their programming expertise in languages, such as R or Python. Emphasis will be placed on developing and sharing code for the wider scientific community through platforms such as GitHub.

The student will learn to communicate their research through publication in peer-reviewed journals and presentation in scientific conferences. By working closely with experts in public health, sequence data, phylogenetic analysis and mathematical modelling, the student will become comfortable working within an interdisciplinary environment and interacting with a diverse scientific team.


A strong academic track record with a 2:1 or higher in a relevant undergraduate degree, or its equivalent if outside the UK. It is also desirable to have a strong performance in a relevant postgraduate degree. Proven experience in one or more of the following is desirable: phylogenetic analysis, mathematical modelling, one scientific programming language (e.g. R, C++, Python). The successful candidate will work in a highly interdisciplinary environment and should be able to work independently and as part of a distributed international team.

Following interview, the selected candidate will need to apply and be accepted for a place on the Usher Institute Global Health PhD programme. Details about the PhD programme can be found here: https://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&edition=2021&id=698

Application procedure

Please provide a CV, a half-page personal statement detailing your research interests and reasons for applying, degree certificate(s), marks for your degree(s) and the names of 2 academic references who can be contacted. All documents should be in electronic format and sent via e-mail to: [Email Address Removed] with the subject line “Phylogenetics PhD application”

The closing date for applications is: 1 March 2022

Funding Notes

Tuition Fees at UK/EU rates (£4,500p.a.) for 3 years, international fees will be waived under the UoE Tuition Fee Contribution Scheme; Additional Programme Costs (£5,000p.a. for wet or dry lab) for 3 years; Conference travel of up to £300p.a. for 3 years; Stipend at RCUK rate (£15,609 p.a.) for 3 years.


Lipsitch M and Siber G (2016) doi: 10.1128/mBio.00428-16
Davies NG, Flasche S, Jit M, Atkins KE (2021) doi: 10.1126/scitranslmed.aaz8690
Dewé TCM, D’Aeth JC, Croucher NJ, (2019) doi: 10.1099/mgen.0.000305

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