Dynamics of Campylobacter and antimicrobial resistance in the food supply chain.

There is increasing interest in food animals as a source of antimicrobial resistant (AMR) bacteria in humans [1, 2]. Campylobacter, the most common bacterial cause of gastroenteritis, has been identified by the World Health Organisation as a high priority antibiotic resistant pathogen, due to extensive quinolone resistance as well as resistance to other common antimicrobials [3]. There are also many biologically and methodologically interesting questions around the development of AMR in Campylobacter, an organism that is found widely in wild animals, food animals and the natural environment, all of these reservoirs acting as sources for human infection. These Questions include:
• How and where does AMR evolve?
• How does AMR spread?
• Does AMR offer a survival advantage in particular niches or affect transmission to humans through the food chain?
As with other bacteria, AMR can be measured directly in Campylobacter and/or inferred from whole genome sequence (WGS) data. We now have access to very extensive WGS data and isolate collections, which also enable Campylobacter population structure and evolution of the bacteria to be described and the levels of gene sharing (Horizontal Gene Transfer, HGT) and its importance to AMR to be measured.

This studentship is linked to a UK Food Standards Agency (FSA) project that provides data from over 5,000 human infections from 1997 to 2018, and from the food chain. This includes hundreds to thousands of genome sequenced isolates from each of a range of animal species, and from different points in the food chain. Campylobacter isolates and WGS data are available from: poultry on farms; abattoirs; retail meat; and human disease. The FSA project is also collating isolates from other projects globally, with extensive international collections available for analysis. This studentship will take a multi-disciplinary approach and will include training in molecular microbiology, bioinformatics, evolutionary analyses, and mathematical modelling.

If you would like to apply please submit an application for a DPhil in Zoology stating Studentship Ref No: BONS01. Application procedure details at: https://www.ox.ac.uk/admissions/graduate/courses/dphil-zoology?wssl=1 . Please note: instead of a research proposal please submit a personal statement.