PhD project: Development of novel approaches to targetting Tuberculosis control in cattle and badgers using mass bacterial deep sequencing

Project description

Whole genome sequencing (WGS) data provide direct evidence of transmission links for infectious diseases 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. Now, government policy 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. 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 analyse the spatial and temporal relationships of already generated M. bovis sampled from cattle and badgers to develop methods to determine local foci of infection and identify genetic signatures consistent with badger dominated, cattle dominated, and balanced transmission patterns.

This position would be based at the Roslin Institute at the University of Edinburgh. See for further information.

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