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EASTBIO: Population functional genomics of the emergence and success of bacterial pathogenic clones

College of Medicine and Veterinary Medicine

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Prof R Fitzgerald , Dr L McNally , Prof M Holden No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Staphylococcus aureus is a major human and livestock pathogen and a member of the priority ESKAPE group of antibiotic-resistant bacterial species. The evolutionary history of S. aureus is marked by the emergence, and dissemination of pathogenic clones associated with community-, hospital, and livestock-associated infections. However, our understanding of the evolutionary events associated with the success of emergent pathogenic clones is very limited. Using an existing database of thousands of S. aureus genome sequences, and population level experimental approaches, we will investigate key evolutionary events that have underpinned the success of S. aureus. Using a combination of phylogenomics, genome-wide association analysis, and high throughput phenotyping of traits such as antibiotic sensitivity and growth dynamics, we will examine the emergence, expansion and decline of selected major pathogenic clones of humans and livestock. In addition, we will compare clonal lineages of S. aureus that regularly switch between different host-species, with those that are largely host-species restricted in order to understand the bacterial basis for this distinct ecology. The genomic and phenotypic data generated will inform models that simulate the dynamics of the emergence and expansion of new pathogen clones. Overall, the project will offer a broad training in phylogenetic and comparative genomic approaches for bacteria and the study will provide broad new insights into the success of one of the most important global pathogens.

Funding information and application procedures:
This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership (DTP) .

EASTBIO Application and Reference Forms can be downloaded via

Please send your completed EASTBIO Application Form along with a copy of your academic transcripts to [Email Address Removed]

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

Funding Notes

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 important that we know from the outset which fees status category applicants fall under when applying to our university.

Please refer to UKRI ( ing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/) and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria (
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