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Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Research: Genomics and Metagenomics of Animal, Environmental and Human Samples to Understand Resistance Gene Transmission Amongst Enterobacteriaceae in Oxfordshire

Project Description

Antimicrobial resistance (AMR) is a major health concern and is exemplified by the rapid emergence of AMR in several key species of the bacterial family of Enterobacteriaceae, such as Escherichia coli and Klebsiella pneumoniae. These bacteria are able to colonise human, animal and environmental niches, but are also a major cause of human disease. The emergence of resistance in these organisms is largely facilitated by intra- and inter-species exchange of AMR genes on mobile genetic vectors, such as plasmids, but it remains unclear where the predominant hotspots of resistance gene emergence are; to what extent species, resistance genes and resistance gene vectors are segregated in various reservoirs versus shared between them; what the population structure of important genera of Enterobacteriaceae is (human and non-human); and how to classify and define plasmid diversity and characterise plasmid evolution.

This project aims to analyse the rich resource of sequence data (metagenomes [n=180], complete bacterial assemblies [n=1000]) being generated as part of the REHAB study ( together with sequences from human bloodstream infections. The project will involve a diverse range of genome sequence processing and analytical disciplines including: evolutionary genomics, bioinformatics, biostatistics, population genetics and comparative genomics.

Potential applicants interested in further information are encouraged to contact Professor Sarah Walker at

Benefits of joining the Medical Research Foundation National PhD Training Programme in AMR Research:
• All PhD projects will be based within interdisciplinary research consortia funded by the UKRI Cross-Council AMR Initiative.
• All students will have access to enhanced training opportunities including residential skills and training courses, cohort-building activities, and annual conferences. All are designed to expose students to a range of discipline-specific languages and interdisciplinary research skills, which are essential for enabling them to thrive as multidisciplinary AMR researchers.
• PhD students will undertake a fully-funded 3-month interdisciplinary AMR project allowing them to work outside of their primary research area or an elective placement in industry, publishing, media, policy development or in AMR-relevant charities and organisations.
• All Medical Research Foundation-funded PhD students will also be part of a wider cohort of 150 PhD students from across the UK who are also studying AMR. The cohort will have access to a bespoke, innovative online learning environment, which will facilitate peer-to-peer networking, question setting and mentoring.

Further information can be found on our website:

Applicants must ensure that they meet the eligibility requirements of the University of Oxford. To qualify for Home tuition fee status, you must be a UK or EU citizen who has been resident for 3 years prior to commencement. Please note that overseas students not eligible for Home (UK/EU/EEA citizens) tuition fee status will be eligible for funding through this Programme but the student must pay the difference between the annual Home tuition fee and the tuition fees required for overseas students. Overseas students should be able to demonstrate adequate financial support to cover the difference between the Home/EU fee and the overseas fee. Applicants are also required to meet the University of Oxford’s English language requirements.


University application guide:

Online applications portal:

Please select DPhil in Clinical Medicine as your programme of study and write: ‘Genomics and Metagenomics of Animal, Environmental and Human Samples to Understand Resistance Gene Transmission Amongst Enterobacteriaceae in Oxfordshire’ under ‘proposed research and title of research project’ in your application form. Please indicate Prof Sarah Walker as proposed supervisor. Proposed funding source should be: Medical Research Foundation National PhD Training Programme in AMR Research. Departmental studentship reference code: 972. Under Statement of study plans/Research Proposal, please state that you are applying for the Medical Research Foundation National PhD Training Programme in AMR Research studentship.

Funding Notes

This is 4 year fully-funded PhD studentship funded jointly by the Medical Research Foundation National PhD Training Programme in AMR (led by the University of Bristol) and the University of Oxford. The studentship covers:

• Annual tuition fees and Oxford college fees at the Home/EU rate
• Stipend at MRC ’plus’ rate £17,000 (2019-20) rising to £18,500 (tax free)
• Yearly travel allowance
• Research costs
• Interdisciplinary 3-month research project/placement allowance

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