2025-26 Project (Atkins & Hué)

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

SUPERVISORY TEAM

Supervisor

Professor Katherine Atkins at LSHTM
Email: katherine.atkins@lshtm.ac.uk

Co-Supervisor

Dr Stéphane Hué at LSHTM
Email: stephane.hue@lshtm.ac.uk

PROJECT SUMMARY

Project Summary

Vaccines against bacterial pathogens have been proposed as a means to combat antibiotic resistant infections. 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.   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.

Project Key Words

Phylogenetic analysis, infectious disease, epidemiology, vaccine

MRC LID Themes

  1. Infectious Disease
  2. Global Health
  3. Health Data Science

Skills

MRC Core Skills

  1. Quantitative skills
  2. Interdisciplinary skills

Skills we expect a student to develop/acquire whilst pursuing this project:

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.

Routes

Which route/s are available with this project?

  • 1+4 = Yes
  • +4 = Yes

Possible Master’s programme options identified by supervisory team for 1+4 applicants:

  • LSHTM – MSc Health Data Science

Full-time/Part-time Study

Is this project available for full-time study? Yes
Is this project available for part-time study? Yes

Location & Travel

Students funded through MRC LID are expected to work on site at their primary institution, meeting – at the minimum – the institutional research degree regulations and expectations. Students may also be required to travel for conferences (up to 3 over the duration of the studentship), and for any required training (for research degree study). Other travel expectations and opportunities highlighted by the supervisory team are noted below.

Primary location for duration of this research degree: LSHTM, London

Travel requirements for this project: Vietnam (Nha Trang), Edinburgh

Eligibility/Requirements

Particular prior educational requirements for a student undertaking this project

  • Minimum LSHTM institutional eligibility criteria for doctoral study.
  • Desirable: previous coding experience; phylogenetic experience.

Other useful information

  • Potential Industrial CASE (iCASE) conversion? = No

PROJECT IN MORE DETAIL

Scientific description of this research project

1. Project objectives 
a. Characterise the spatial epidemiology of Streptococcus pneumoniae drug resistance within the high burden settings of Nha Trang, Vietnam. 
b. Evaluate the local and regional spread of Streptococcus pneumoniae drug resistance using phylogenetics. 
c. Quantify the impact of pneumococcal conjugate vaccine on the spread of Streptococcus pneumoniae drug resistance. 

2. Techniques to be used 
The project will use an interdisciplinary combination of genetic sequence data analysis, epidemiology, and phylogenetic analysis. 

3. Confirmed availability of any required databases or specialist materials 
This project will use already-collected rich sequence data and complementary epidemiological data from a multi-year cluster randomized trial for a pneumococcal conjugate vaccine (PCV) in Vietnam. 

4. Potential risks to the project and plans for their mitigation
No foreseeable risks. The data are rich with numerous scientific questions that can be investigated.

Further reading

Relevant preprints and/or open access articles:
(DOI = Digital Object Identifier)

Additional information from the supervisory team

The supervisory team has provided a recording for prospective applicants who are interested in their project. This recording should be watched before any discussions begin with the supervisory team.

Atkins-Hué recording

MRC LID LINKS

Comments are closed.