The role of mobile DNA in the evolution, fitness, AMR and pathogenicity of avian Escherichia coli populations

This studentship aims to investigate antimicrobial resistance (AMR) transmission within poultry microbiota to further understand the impact of AMR transmission on pathogen fitness, and develop strategies to reduce the impact of AMR. 

Start date

1 April 2022


3.5 years

Application deadline

Funding source

University of Surrey

Funding information

Fully funded, including UK fees, stipend (£15,609 for 2021/22) and training.


Applications are invited for a fully-funded 3.5 year PhD studentship to commence in April 2022 supervised by Dr Jai Mehat.

Antimicrobial resistance (AMR) presents an immediate threat to global health.

Intensive poultry production is a significant animal-human interface at which pathogens and AMR determinants may be introduced into the human food-chain. Considering there are 26 billion domesticated chickens in production globally, the chicken gut microbiota represents an important and understudied reservoir that may facilitate spill-over of AMR determinants into the human niche, and novel interventions are required to control this.

E. coli is a pioneer constituent of the avian and mammalian gut, however a minority of pathogenic and multi-drug resistant (MDR) E. coli lineages are responsible for enormous health burdens and economic losses worldwide.

We have previously characterised the avian E. coli lineages associated with highest pathogenic potential, and preliminary work has implicated plasmid-encoded class 1 integrons as drivers for the acquisition and dissemination of MDR genes in these populations.

This PhD studentship aims to assess the impact of MDR gene acquisition events on the fitness, metabolism, and pathogenicity of Escherichia coli at the animal-human interface, in order to evaluate the risk of emerging MDR and pathogenic E. coli lineages. Additionally, this project will explore the use of probiotic bacteria as a means to reduce emergence of MDR E. coli in this niche.


Initial studies will focus on characterising the distribution of multi-drug resistance determinants in avian E. coli populations. Suitable plasmids encoding Class 1 integrons will be identified and selected.

The studies will then progress to assess the impact of transmission of these plasmids between defined E. coli genetic backgrounds relevant to avian and human health, using an in vitro avian gut model, as well as assessing the feasibility of employing probiotics as a means of mitigation.

Related links

School of Biosciences and Medicine School of Veterinary Medicine


Jai W. Mehat, Arnoud H. M. van Vliet & Roberto M. La Ragione (2021) The Avian Pathogenic Escherichia coli (APEC) pathotype is comprised of multiple distinct, independent genotypes, Avian Pathology, 50:5, 402-416, DOI: 10.1080/03079457.2021.1915960

Michael Hornsey, Jonathan W. Betts, Jai W. Mehat, David W. Wareham, Arnoud H. M. van Vliet, Martin J. Woodward, Roberto M. La Ragione (2019) Characterization of a colistin-resistant Avian Pathogenic Escherichia coli ST69 isolate recovered from a broiler chicken in Germany, In: Journal of Medical Microbiology68(1)pp. 111-114 Microbiology Society DOI: 10.1099/jmm.0.000882

Eligibility criteria

The successful candidate will hold good first degree (2:1 or above) in a relevant subject such as biology, microbiology or molecular biology. An MSc in a relevant subject would be desirable. Experience of microbial genomic analysis and practical microbiology will be advantageous. The successful applicant will join a diverse team working at the intersection of zoonoses, AMR and novel therapeutic interventions. The student will be based in the School of Biosciences and Medicine, and work closely with researchers from the School of Veterinary Medicine.

English language requirements 

IELTS minimum 6.5 or above (or equivalent) with 6.0 in each individual category.

How to apply

Applications should be submitted via the Biosciences and Medicine PhD programme page on the "Apply" tab. Please clearly state the studentship title and supervisor on your application.

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Application deadline

Contact details

Jai Mehat

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