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

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

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 Alliance was further strengthened in 2018 via establishment of the Centre for Sustainable Aquaculture Futures (see: https://www.exeter.ac.uk/saf/). A major component of the Alliance is to support joint PhD studentships.

In accordance, we are pleased to announce the intention to fund a new PhD project to start in September 2023. This project is one of two projects that are in competition for funding from the University of Exeter and Cefas.

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.

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