MRC DiMeN Doctoral Training Partnership: What features of opportunistic pathogens makes them likely to harbour antimicrobial resistance elements?


Antimicrobial resistance (AMR) is a major challenge for modern medicine, with almost 1.3m deaths due to AMR infection in 2019. This public health crisis is largely driven by mobile genetic elements (MGEs), which can effectively transfer AMR determinants into pathogens even without direct antibiotic selection. Different bacteria vary in their susceptibility to acquiring, harbouring, and disseminating resistance MGEs, but our lack of understanding of the underlying mechanisms hampers our ability to predict and stem the emergence of new multi-drug resistant pathogens. In this project, you will determine patterns of MGE susceptibility across the ‘critical’ priority opportunistic pathogen Pseudomonas aeruginosa — including samples from clinical trials that tracked pathogen evolution during antibiotic treatment of cystic fibrosis patients — and use a combination of functional genomics and machine learning to unpick the underlying mechanisms that favour MGE carriage and spread.

This project combines wet-lab and computational approaches. You will be trained in microbial culture and molecular biology techniques as well as computational approaches, including transcriptomic analysis and machine learning. Background in any of these subjects would be useful, but more important are enthusiasm for microbial evolution/AMR, self-motivation, and the drive to develop an independent research project. Students will also gain training in general research skills such as scientific writing, presentation, literature reviewing, and statistical analysis, developing skills that will place them in an excellent position for a future scientific career. The project will be co-supervised by Dr. Jamie Hall, Dr. Marcus Blagrove, and Dr. Jo Fothergill at the University of Liverpool as part of the DiMeN Doctoral Training Partnership.

Applicants should generally have an upper second or first class degree in biological sciences plus additional experience such as a Master’s or employment in a research environment. Please get in touch by email if you have any questions about this project or your suitability for the position: pre-application enquiries are encouraged.

Benefits of being in the DiMeN DTP:

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle, York and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here:

Further information on the programme and how to apply can be found on our website:



Open to students worldwide

Funding information

Funded studentship

Studentships are fully funded by the Medical Research Council (MRC) for 4yrs. Funding will cover tuition fees, stipend and project costs. We also aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of full studentships to international applicants. Please read additional guidance here: View Website
Studentships commence: 1st October 2023
Good luck!



Hall JPJ, Wright RCT, Harrison E, Muddiman KJ, Jamie Wood A, Paterson S, et al. Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLoS Biol 2021; 19: e3001225
Cazares A, Moore MP, Hall JPJ, Wright LL, Grimes M, Emond-Rhéault J-G, et al. A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas. Nat Commun 2020; 11: 1370
Wardeh M, Baylis M, Blagrove MSC. Predicting mammalian hosts in which novel coronaviruses can be generated. Nat Commun 2021; 12: 780.