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Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Research: Predicting empiric antimicrobial prescribing from local surveillance of active and potential antimicrobial resistance mechanisms

Project Description

The majority of antimicrobials (AMs) that are prescribed are initiated empirically for presumed bacterial infection in the absence of a microbiological culture with associated AM sensitivity testing. The initial empiric AM choices for the syndromic management of bacterial infections are informed by an understanding of local phenotypic AM resistance (AMR) patterns from various clinical samples. To optimise empirical AM prescribing there is a clear need to better characterise circulating local AMR mechanisms, the interplay between mechanisms and how they manifest as phenotypic AMR, and their clinical impact on patient outcome.

This project will use Whole Genome Sequencing (WGS) of bacterial isolates from bloodstream infection (BSI) and urinary tract infections (UTI) from patients who live in Bristol. Using available phenotypic AMR data and patient outcome data, together with laboratory experimentation on the co-evolution of AMR from different origins, the outputs of this project will be:

Data on the rates of co-occurrences of AMR genes allowing the optimisation of empiric AM selection. We hypothesise that the added value of this WGS approach is that it will allow us not only to consider phenotypic AMR, but “potential” AMR carried by a local bacterial population, which might quickly become phenotypically relevant. This will improve guidance of empiric AM choice to best avoid the potential development as well as the actual presence of AMR.

The project would suit someone with a microbiology/molecular biology background who wants to do laboratory experiments and learn bioinformatics, whilst working alongside clinicians and clinical scientists to make a difference to patient care.

Potential applicants interested in further information are encouraged to contact Professor Matthew Avison 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 Bristol. 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 Bristol’s English language requirements.


As part of your application, you need to choose: Faculty of Life Sciences under the ‘Faculty’ section, and Cellular and Molecular Medicine 4-year PhD programme under the ‘programme choice’ section. Additionally, under ‘funding’ and ‘Research Details’ section, please indicate that you are applying for a Medical Research Foundation National PhD Training Programme in AMR Research funded project and give the project title and names of the supervisors.

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 Bristol. 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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