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Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Research: Elucidating E. coli Bacteraemia Resistance, Risk Factors and Outcomes: Linking Bacterial Genomics, Case Note Review and Health Informatics

Project Description

Antimicrobial resistance (AMR) is an increasing public health threat and resistance among E. coli is of increasing global concern. To design measures to tackle AMR, a better understanding of the contribution of bacterial genomic and patient factors in the development and spread of AMR is critical.

The aim is to link whole genome sequencing (WGS) of E. coli isolates from bloodstream infections (bacteraemia) to data from the source patient’s hospital notes and electronic health record (EHR) to investigate bacterial and patient factors associated with resistance and clinical outcome.

This project involves WGS of all E. coli bacteraemia isolates over a one-year period from residents of a complete geographic area (in addition to standard NHS culture and sensitivity testing) and collecting information from the patients’ inpatient medical records, which will then be linked to EHR data. Analysis of the WGS data will characterise genomic resistance and virulence traits and identify any clusters and potential transmissions using phylogenomic methods. Analysis of the linked data will investigate epidemiological evidence of transmission, associations between genotypic and phenotypic resistance, patient risk factors for resistant infections and adverse outcomes, and interactions between patient and bacterial factors.

This project will appeal to students with cross-disciplinary interests in infectious diseases, bacterial genomics, epidemiology, clinical microbiology and infection control.

Potential applicants interested in further information are encouraged to contact Dr Charis Marwick.

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 Dundee. 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 Dundee’s English language requirements.

Applicants should have a Master’s level qualification and evidence of research experience (e.g. through a Master’s degree project).


To apply please send a cover letter, curriculum vitae and two references to:

Please state clearly in your cover letter that you are applying for a Medical Research Foundation National PhD Training Programme in AMR Research funded project. Eligibility criteria and more information about postgraduate study at the University of Dundee are available here: and the UCAS online application (which the successful candidate will be required to complete after interview and offer of the studentship) is available here:

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 Dundee. The studentship covers:

• Annual tuition 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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