EPSRC DTP PhD project: The prevalence and persistence of antibiotic resistance plasmids in wastewater.

   Department of Life Sciences

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  Prof Edward Feil  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

The University of Bath is inviting applications for the following PhD project commencing on 30 September 2024 under the supervision of Prof Edward Feil in the Department of Life Sciences, with co-supervison from Prof Barbara Kasprzyk-Hordern in the Department of Chemistry and Dr Theresa Smith in the Department of Mathematics.

Eligible applicants will be considered for a fully-funded studentship – for more information, see the Funding Notes section below.

Overview of the Research:

The rapid spread of antimicrobial resistance (AMR) around the globe represents a major public health and economic burden. As resistant bacteria can also cause commercially significant disease in livestock and other food animals, as well as humans, there are additional major challenges for food security. Mitigating the spread of resistance requires more sagacious usage of antibiotics both in clinical and agricultural settings, but close epidemiological surveillance is also needed to understand the scale of the challenge, target interventions and measure their effectiveness. Wastewater provides a powerful resource for surveying the overall abundance of AMR within a population, as well providing broader indicators of population health. The development of the infrastructure required for large-scale wastewater-based epidemiology (WBE) accelerated rapidly during the Covid-19 pandemic.

However, tracking the spread of AMR remains challenging conceptually as well as logistically. Typically, surveillance can be carried out on the level of resistant strains, using whole genome sequencing, or individual antibiotic resistant genes (ARGs), using PCR or metagenomics approaches. However, ARGs are often carried on plasmids, which play a central role in spreading resistance between different strains of bacteria, and even species, and in disseminating ARGs into the broader environment. AMR plasmids are far more difficult to characterise and track than bacteria or individual genes, and much remains unclear as to how these elements persist and transmit within the environment.

This project will use long-read metagenomic sequencing on multiple samples of wastewater influent representing contrasting sites in the Avon catchment. These samples were collected as part of a Covid-19 monitoring project over the course of a full year. We will identify and characterise key AMR plasmids in these samples and, by considering data on the chemical properties of the samples and other relevant parameters, we will statistically identify key drivers for geographical and temporal trends in AMR plasmid abundance. The project will this be multidisciplinary, involving bioinformatics, chemical analysis (mass spectrometry) and statistical modelling.

Project keywords: Antimicrobial resistance, plasmids, wastewater, bioinformatics, antibiotics.

Candidate Requirements:

Applicants should hold, or expect to receive, a First Class or good Upper Second Class UK Honours degree (or the equivalent) in the Life Sciences. Experience with ‘R’ or other statistical packages would be beneficial. A master’s level qualification would also be advantageous but is not essential.

Non-UK applicants must meet our English language entry requirement.

Enquiries and Applications:

Applicants are encouraged to contact Prof Edward Feil on email address [Email Address Removed] before applying to find out more about the project and to discuss their suitability for the role.

Formal applications should be made via the University of Bath’s online application form for a PhD in Biology.

In the ‘Funding your studies’ section of the application form, please select ‘EPSRC DTP’ from the first drop-down menu. In the ‘Your PhD project’ section, please quote the project title and lead supervisor’s name in the appropriate fields. Failure to complete these steps will cause a delay in processing your application and may cause you to miss the deadline.

More information about applying for a PhD at Bath may be found on our website.

Equality, Diversity and Inclusion:

We value a diverse research environment and aim to be an inclusive university, where difference is celebrated and respected. We welcome and encourage applications from under-represented groups.

If you have circumstances that you feel we should be aware of that have affected your educational attainment, then please feel free to tell us about it in your application form. The best way to do this is a short paragraph at the end of your personal statement.

Biological Sciences (4) Chemistry (6) Environmental Sciences (13) Mathematics (25)

Funding Notes

Candidates applying for this project may be considered for a 3.5-year Engineering and Physical Sciences Research Council (EPSRC DTP) studentship. Funding covers tuition fees, a stipend (£18,622 per annum, 2023/24 rate) and research/training expenses (£1,000 per annum). EPSRC DTP studentships are open to both Home and International students; however, in line with guidance from UK Research and Innovation (UKRI), the number of awards available to International candidates will be limited to 30% of the total.


Gibbon MJ, Couto N, David S, Barden R, Standerwick R, Jagadeesan K, Birkwood H, Dulyayangkul P, Avison MB, Kannan A, Kibbey D, Craft T, Habib S, Thorpe HA, Corander J, Kasprzyk-Hordern B, Feil EJ. A high prevalence of blaOXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England. Microb Genom. 2021 Jan 8. doi: 10.1099/mgen.0.000509

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