EASTBIO: Development of novel approaches to targetting Tuberculosis control in cattle at the University of Edinburgh

Supervisors:  Professor Rowland Kao, Anthony O’Hare, Dr. C. Benton, Dr. Eleftheria Palkopoulou.

Whole genome sequencing (WGS) data has transformed our understanding how pathogen emerge, spread and are maintained. They provide direct evidence of transmission links at a very fine scale, and make possible high resolution estimates of when an emergent outbreak started, and what the rate of spread is between geographical regions or between species. They are invaluable for studying multi-host pathogens, particularly involving wildlife. However better methods of analysis are still needed, in turn requiring good study populations to develop them on. One exemplar with many ideal features is bovine Tuberculosis in British and Irish cattle and badgers (bTB, caused by Mycobacterium bovis), where there are many excellent, dense datasets ideal for developing new methods and insights.

Use of WGS for bTB is especially valuable, because the disease places a high burden on the farming community, and the use of culling to control Tb in badgers (widely used in much of Britain and Ireland at least until now) has been controversial. The UK government is following a TB strategy that aims for official disease freedom by 2038 (https:///...e-status-for-england). To achieve this, it is moving away from badger culling and is instead relying on a combination of cattle and badger directed control options, and it is increasingly looking to the potential for vaccination to control the disease in both species. However, for these measures to succeed, we need a deeper understanding of how badger and cattle combine to maintain Tb in cattle, as this determines, for example, minimum requirements for vaccine coverage in either species, and how it should be targeted (how many, and over what area?).

Project candidates will have good evidence of mathematics or statistics skills and preferably experience of computer programming, They will use existing datasets and novel ones generated over the course of this project to analyse the spatial and temporal relationships of M. bovis sampled from cattle and badgers and compared to datasets where samples from cattle alone are available. They will develop methods to determine local foci of infection and identify genetic signatures consistent with badger dominated, cattle dominated, and balanced transmission patterns. The project has the potential to inform appropriate targeting of future control of M. bovis transmission in the two species. The student will learn new quantitative methods as well as gain experience of data interpretation at the national reference laboratory and a long term (over four decades long) badger study site.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership (DTP) http://www.eastscotbiodtp.ac.uk/how-apply-0 .

EASTBIO Application and Reference Forms can be downloaded via   http://www.eastscotbiodtp.ac.uk/how-apply-0

Please send your completed EASTBIO Application Form along with a copy of your academic transcripts to [email protected]

You should also ensure that two references have been send to [email protected]  by the deadline using the EASTBIO Reference Form.

This opportunity is open to UK and international students and provides funding covering stipend and UK level tuition fees.  The University of Edinburgh covers the difference between home and international fees meaning that the EASTBIO DTP offers fully-funded studentships to all appointees.  There is a cap on the number of international students the DTP recruits.  It is therefore important for us to know from the outset which fees status category applicants will fall under when applying to our university.

Please refer to UKRI websiteand Annex B of the UKRI Training Grant Terms and Conditionsfor full eligibility criteria.

Closing Date: 16th December 2021