PhD project: Leveraging pathogen genomics and phylodynamics to control endemic anthrax

Recent advances in sequencing technology have revolutionised our ability to track infectious disease dynamics using pathogen genomes, such as during outbreak investigations [1]. However, these tools remain underutilised for addressing endemic disease threats, especially those affecting human and animal health in low-resource settings. Anthrax is a classic example of a neglected bacterial zoonosis, affecting marginalised communities in many parts of the global south, including much of Sub-Saharan Africa [2]. It causes significant mortality in people as well as livestock losses, but tends to be undiagnosed and underreported [3]. Although vaccination of livestock plays a key role in preventing infection in both people and animals, it is often not affordable. Moreover, because the spores of the anthrax bacterium Bacillus anthracis can remain infectious within the environment for decades, it is not clear how long livestock vaccination would have to be maintained before a measurable reduction in infection risk is achieved. Obtaining genome data from detected cases, and incorporating genomic and epidemiological data into phylodynamic models [4], provides a novel and powerful means to track residual anthrax transmission and quantify progress towards its elimination.

This project aims to create the necessary framework for guiding anthrax control programmes in endemic settings through the use of pathogen genomics and phylodynamic modelling.

Specific objectives are to:

1. Extend current analytical tools and molecular clock models to accommodate the alternation between extended environmental persistence and periodic rapid replication typical for B. anthracis;
2. Develop a simulation model combining genomic, spatial, temporal and epidemiological information to examine the effect of vaccination on B. anthracis genetic diversity and transmission in silico;
3. Validate this model by generating genomic data obtained during a livestock vaccination program expected to start in the study area in 2020.

Supervisors:
Dr Roman Biek (Reader, University of Glasgow)’s primary research interest is infectious disease ecology. He has wide-ranging experience in quantitative and phylogeographic approaches incorporating both spatio-temporal and genomic sequence data.

Dr Samantha Lycett (Group Leader, University of Edinburgh)’s expertise is in pathogen phylodynamics and population modelling. She brings to the project extensive experience in developing new computational tools and models to gain epidemiological insights from pathogen genome data and guide control efforts (e.g. eradication of bovine diarrhoea virus from UK farms).

Dr Taya Forde (BBSRC Future Leader Fellow, University of Glasgow) is a molecular epidemiologist with a particular interest in the transmission dynamics of bacterial zoonoses. She has led the collection of long-term genomic data from cases of animal and human anthrax in Tanzania and brings expertise in the genomics of Bacillus anthracis.

Dr Tiziana Lembo (Senior Lecturer, University of Glasgow) is a field veterinary scientist with an interest in applied infectious disease epidemiology in complex multi-host environments. She has a long track record of productive collaborative research in Tanzania, including in the area of One Health interventions, and has been helping support Tanzanian stakeholders in developing vaccination campaign strategies.

The student will thus benefit from a highly multidisciplinary supervisory team. They will be primarily based at the University of Glasgow’s Institute of Biodiversity Animal Health and Comparative Medicine (BAHCM), at the main campus (Gilmorehill). The Institute provides a rich and collaborative research environment with a strong track record of applying evolutionary and quantitative approaches to One Health problems.
Combined, this supervisory group has the available research platform and expertise to guide the student in developing novel approaches that capitalise on epidemiological and genomic data to gain insights into pathogen dynamics towards informing anthrax control efforts. The student will greatly benefit from expertise, networks and opportunities at both Universities. The student will develop core skills in bioinformatics, phylodynamics and population modeling and gain familiarity with the fields of bacterial genomics, neglected zoonotic diseases, One Health and intervention studies.

The project builds on robust partnerships and research platforms established in northern Tanzania by the Glasgow supervisors, including existing genomic and epidemiological data. It also brings together highly complementary expertise of researchers at the University of Glasgow and the University of Edinburgh to provide practical solutions to a One Health challenge. There is also an element of translational and impact-driven research by applying the research outcomes to inform vaccination strategies by our partners in the Tanzanian Government.

Eligibility
Open to UK, EU and international applicants.

Academic qualifications
While not a strict requirement, a postgraduate Master’s degree would be an asset. Relevant subjects would include health sciences, bioinformatics, computer science, mathematics, or geosciences. An undergraduate degree with scientific and quantitative components is assumed.

Experience
Experience working with sequence data and/or with mathematical modelling would be an asset.

Skills/Attributes
The student should demonstrate a willingness and ability to learn new skills. They should have an interest in developing data science and computational skills, in infectious disease genomics, and in practical issues around disease control in natural systems.

Key facts
Tuition Fee and 4 years' stipend at UKRI rates (estimated to be in the region of £15,245 for 2020/21)
Annual research support budget of £2,000
Travel support costs of £1,000

Application deadline: 12 noon, Monday 13 January 2020

Information on how to apply available at
https://www.gla.ac.uk/research/ourresearchenvironment/prs/uofguofedinphdstudentships/onehealth/#d.en.622924

For further information, contact roman.biek@glasgow.ac.uk

References

1. Kao R, Haydon D, Lycett S, Murcia P. (2014) Supersize me: how whole-genome sequencing and big data are transforming epidemiology. Trends in Microbiology 22(5): 282-91.
2. Carlson et al. (2019) The global distribution of Bacillus anthracis and associated anthrax risk to humans, livestock and wildlife. Nature Microbiology 4(8):1337-43.
3. WHO (2006) The Control of Neglected Zoonotic Diseases: A route to poverty alleviation.
4. Biek R et al. (2015) Measurably evolving pathogens in the genomic era. Trends in Ecology & Evolution 30(6): 306-13.