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Award details

Are shellfish hotspots for AMR evolution and transmission? [microbiology, evolutionary biology, bio-clinical science, public health, aquaculture] – PhD (Funded) Ref: 4379

About the award


Lead Supervisor:

Professor William Gaze, University of Exeter 


Professor Angus Buckling, University of Exeter 

Dr Anne Leonard, University of Exeter 

Dr David Verner-Jeffreys, Centre for Environment, Fisheries & Aquaculture Science

Dr Craig Baker-Austin, Centre for Environment, Fisheries & Aquaculture Science


Environment and Sustainability Institute, Penryn Campus, Cornwall and Cefas in Weymouth

The Centre for Environment, Fisheries & Aquaculture Science (Cefas) and the University of Exeter have a Strategic Alliance that aims to combine the complementary capabilities and perspectives of both organisations. This project is one of four on the theme of sustainable, healthy seafood that are in competition for funding from the University of Exeter and Cefas for two PhDs. 

Project Description: 

Globally, antimicrobial resistance (AMR) has emerged as a critically important health threat. Drug resistant infections are rising with estimates suggesting up to 10 million fatalities each year by 2050 (O’Neill, 2016). AMR is a true One Health challenge, with the environment critical to the emergence and dissemination of AMR bacteria, and the resistance genes they harbour, to humans and animals. Aquatic systems likely represent a particularly important milieu for the environmental release, mixing, evolution and spread of AMR bacteria and resistance genes.

Shellfish are recognised as an increasingly important food source, necessary to support the rising global demand for aquatic protein. However, there are known human health risks associated with bivalves because of their propensity to bioaccumulate pathogens, toxins and chemicals present in the surrounding environment. These risks likely also extend to concentration of AMR bacteria, genes and antimicrobials released into the environment from sources such as wastewater treatment plants and combined sewer overflows. This project will utilise a combination of next generation sequencing, experimental and quantitative approaches to investigate: 1) the prevalence and diversity of AMR bacteria in bivalve molluscs, 2) the evolution of AMR in the shellfish microbiome and 3) the risk posed to human health in terms of estimating transmission risk using approaches from quantitative microbial risk assessment (QMRA). 

First oysters and mussels will be sampled from a variety of locations and the AMR "resistome" characterised using next generation sequencing and metagenomic approaches. Evolution experiments will use a combination of genetically tagged bacteria/plasmids to study the frequency of gene transfer in a live bivalve shellfish model system relative to the surrounding water. Horizontal gene transfer (HGT) between human associated Enterobacteriaceae and indigenous marine Vibrio spp. will be studied using a fluorescent plasmid reporter system to differentiate plasmid donors and recipients. We will investigate the effects of differing selection pressure (e.g. presence/absence of low concentrations of antibiotics and heavy metals) on the evolution of resistance in the bivalve microbiome. Transmission studies will focus on estimation of human exposure based on individual and population level consumption data as a function of AMR bacteria / resistance gene prevalence and diversity. If time allows this work will be extended to a cohort study of shellfish consumers compared to controls, focusing on gut colonisation of individuals with 3rd generation cephalosporin resistant E. coli which is the WHO recommended One Health AMR surveillance target.

This PhD proposal is data driven, translational and truly interdisciplinary combining aspects of microbiology, molecular biology, bioinformatics, evolutionary ecology, epidemiology and risk assessment. The student will be based at the University of Exeter's Cornwall Campus and Cefas in Weymouth. The large, international and well-funded groups of the Exeter PIs share a large state-of-the art laboratory, providing extensive opportunities for skills development and network building. 

This award provides annual funding to cover Home tuition fees and a tax-free stipend.  For students who pay Home tuition fees the award will cover the tuition fees in full, plus at least £15,609 per year tax-free stipend.

Entry requirements

Applicants for this studentship must have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK, in an appropriate area of science or technology.  

Students who pay international tuition fees are eligible to apply, but should note that the award will only provide payment for part of the international tuition fee and no stipend.  

The conditions for eligibility of home fees status are complex and you will need to seek advice if you have moved to or from the UK (or Republic of Ireland) within the past 3 years or have applied for settled status under the EU Settlement Scheme.

International applicants need to be aware that you will have to cover the cost of your student visa, healthcare surcharge and other costs of moving to the UK to do a PhD. 

If English is not your first language you will need to have achieved at least 7.0 in IELTS and no less than 6.0 in any section by the start of the project.  Alternative tests may be acceptable (see

How to apply

In the application process you will be asked to upload several documents.  

  • CV
  • Letter of application (outlining your academic interests, prior research experience and reasons for wishing to undertake the project).
  • Transcript(s) giving full details of subjects studied and grades/marks obtained (this should be an interim transcript if you are still studying)
  • Names of two referees familiar with your academic work. You are not required to obtain references yourself. We will request references directly from your referees if you are shortlisted.
  • If you are not a national of a majority English-speaking country you will need to submit evidence of your proficiency in English.

The closing date for applications is midnight on 7 January 2022.  Interviews will be held in early February 2022. 

If you have any general enquiries about the application process please email or phone 0300 555 60 60 (UK callers) +44 (0) 1392 723044 (EU/International callers).Project-specific queries should be directed to the main supervisor


Application deadline:7th January 2022
Value:3.5 year studentship: Home tuition fees and an annual maintenance allowance at current Research Council rate. Current rate of £15,609 per year.
Duration of award:per year
Contact: PGR Admissions Team