A Population Genomics Study of Natural Selection of Staphylococcus epidermidis

Our research focuses on the bacterial species Staphylococcus epidermidis. S. epidermidis is a common member of the human skin microbiome, but also an increasingly common cause of hospital-associated infections. Together with S. aureus, S. epidermidis is responsible for ~27% of all bacterial bloodstream isolates in the UK and 11% of all healthcare-associated infections in the United States. In certain patients S. epidermidis is even more prevalent as a source of infection than its more pathogenic relative S. aureus. With an ageing population and resulting increase in the use of devices such as intravenous catheters, S. epidermidis is becoming increasingly medically relevant.
The S. epidermidis global population is comprised of three main clades, which in turn consist of six genetic clusters (GCs). Clade A comprises GC5, which is isolated almost exclusively from hospital sources, in both infection-causing and contaminant samples, and GC1 and GC6, possibly more generalist GCs. Clade B comprises GC2 and GC4, which may represent strains from an as yet poorly sampled alternative ecological niche.
Your PhD will investigate S. epidermidis’ evolutionary history, focusing on one or more of S. epidermidis’ GCs, and the events and/or genes that make this species successful in both a hospital setting and as a member of the human skin microbiome. The project will comprise a blend of both wet lab and bioinformatics techniques, including whole genome sequencing and a range of molecular biology techniques. You will be based at NTU’s Clifton campus, where research facilities include a well-equipped microbiology lab, next-generation sequencing laboratory and associated computing resources. As part of the microbiology team, you will be joining a small but close-knit and supportive cohort of PhD students.
When applying, please explain why you are interested in this project and whether you have bioinformatics and/or wet lab expertise.

For informal queries about the project, please contact Dr Jonathan Thomas – [Email Address Removed]

Applicants for PhD or MPhil should normally hold a first or upper second class honours degree of a UK university or an equivalent qualification in Microbiology or other relevant biology-based degree, or a lower second class honours degree with a master’s degree at Merit level of a UK university or an equivalent qualification.
A familiarity with Linux-based computing environments is desirable but not essential.