Characterisation of Antimicrobial Resistance Gene Dissemination in Enterobacteriaceae from Farms in Oxfordshire using Whole Genome Sequencing

This project is offered as part of the Medical Research Foundation National PhD Training Programme in AMR: https://www.findaphd.com/search/PhDDetails.aspx?CAID=3755

Antimicrobial resistance (AMR) is one of the biggest healthcare threats affecting our ability to treat disease in humans and animals, and impacts on the environment. This PhD will build on work underway in REHAB (http://modmedmicro.nsms.ox.ac.uk/rehab/), a multi-disciplinary, multi-institute project sampling humans, animals and the environment in Oxfordshire, to understand the spread of AMR in Enterobacteriaceae and factors influencing its dissemination. This PhD will focus on the animal compartment, which may be a reservoir of important AMR genes present in humans, such as those found in cefotaxime-resistant Enterobacteriaceae (cfrE), and may be linked to multidrug resistance. Faeces from animals on farms identified as positive or negative for cfrE will be characterised further by isolating cfrE and performing Next Generation Sequencing to identify AMR genes, plasmids and mobile genetic elements, and compared with disease-causing isolates from humans to understand dissemination to humans. Bacterial enumeration will be performed to determine cfrE prevalence, and gauge sensitivity of detection and within-herd spread at different seasons. Analysis of molecular/microbiological data and data collected from farm questionnaires will help identify risk factors influencing within-herd dissemination of important AMR elements, and spread to humans. The successful candidate will be enrolled at the University of Oxford’s Medical Sciences Doctoral Training Centre for additional training opportunities and local student cohort activities; however, much of the project will be carried out at the APHA site in Surrey.

Oxford application guide: https://www.ox.ac.uk/admissions/graduate/applying-to-oxford/application-guide?wssl=1

Apply here: https://evision.ox.ac.uk/urd/sits.urd/run/siw_ipp_lgn.login?process=siw_ipp_app_crs

This application follows a similar administrative process as the NDM Prize studentships (https://www.ndm.ox.ac.uk/for-applicants), although it is a separate programme. On your application, the Course Code is “RD_CM1” and the Programme description is “DPhil in Clinical Medicine”. Under Proposed field and title of research project enter “NDM Prize Studentship Competition.” Under Proposed Supervisor name enter the project numbers and names of the supervisors involved in the Medical Research Foundation National PhD Training Programme in AMR Research/REHAB projects. The Advertised Reference Code for applications is “12CLINMED0”. 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.