PhD Study : Ecology and evolution of antibiotic resistance in aquatic environments

Summary

Background:

The emergence of superbugs as bacteria with resistance against multiple or all available antibiotics has the potential to cause a global health crisis. While their frequency of occurrence has been well documented in medical care, natural environments have only just started to come under scrutiny as likely sources of multiple resistance against antibiotics (Berendonk et al., 2015). In particular, aquatic systems receive transfers from multiple sources exposed to waste from treatments with antibiotics, which also may contain live resistant bacteria or their resistance genes. The ecosystem response remains largely unknown. Experimental evidence suggests that the response is complex and variable depending on the type of antibiotics, bacteria, aquatic organisms and abiotic factors, which are interacting.

This project will investigate the role of ecological processes in accumulation, persistence and proliferation of antibiotic resistance in aquatic environments with a particular focus on the facilitation of resistance transfer. With complementary investigations at bench and field scale it will expand on current UU research, which has provided a proof of principle for filter feeding as one type of biotic interaction with such a facilitating effect (e.g. Olanrewaju et al., 2019). It will also explore related processes of relevance to the resistome of aquatic sediments.

Research objectives:

1) Review of the effects of aquatic bacterivores on aquatic systems and on population dynamics of bacteria pheno- and genotypes

2) Development of model systems for the experimental investigation of ecological interactions with effects on antibiotic resistance

3) Investigation of the facilitation of microbial resistance transfer by single species of aquatic invertebrates and protozoa

4) Investigation of the persistence of multi resistant bacteria in facilitating organisms and of the potential transfer to their predators

5) Exploration of the environmental constraints for biotic facilitation of resistance transfer

6) Evolution of antibiotic resistance in bacteria of aquatic environments under selected environmental constraints

7) Field studies of the resistome in sediments subject to transfers from aquatic organisms with proven potential (Objectives 1, 3) for facilitation of antibiotic resistance transfer

Methodology:

The investigation will employ methods of hydrobiology (microcosm studies of filtration rates, microscopy), classical microbiology (e.g. resistance profiles) and molecular biology (e.g. q-PCR and metagenomics).

Impact: Knowledge of ecological processes contributing to accumulation, persistence and proliferation of antibiotic resistance in aquatic systems is highly relevant for environmental regulators and water managers. Project results will inform strategies for the monitoring of antibiotic resistance in aquatic environments, in particular where such efforts focus on the sampling of sediments. Furthermore, the investigation of aquatic organisms, which concentrate waterborne bacteria, and food chain effects will yield relevant information for food safety.

References:

Berendonk TU, Manaia CM, Merlin C, Fatta-Kassinos D, Cytryn E and Walsh F., et al. (2015). Tackling antibiotic resistance: the environmental framework. Nat Rev Microbiol. 2015;13:310–317.

Olanrewaju TO, McCarron M, Dooley JSG and Arnscheidt J (2019). Transfer of antibiotic resistance genes between Enterococcus faecalis strains in filter feeding zooplankton Daphnia magna and Daphnia pulex. Sci Total Environ. 659: 1168–1175

Essential criteria

Applicants should hold, or expect to obtain, a First or Upper Second Class Honours Degree in a subject relevant to the proposed area of study.

We may also consider applications from those who hold equivalent qualifications, for example, a Lower Second Class Honours Degree plus a Master’s Degree with Distinction.

In exceptional circumstances, the University may consider a portfolio of evidence from applicants who have appropriate professional experience which is equivalent to the learning outcomes of an Honours degree in lieu of academic qualifications.

• A comprehensive and articulate personal statement

Desirable Criteria

If the University receives a large number of applicants for the project, the following desirable criteria may be applied to shortlist applicants for interview.

• First Class Honours (1st) Degree
• Masters at 65%
• Research project completion within taught Masters degree or MRES
• Practice-based research experience and/or dissemination
• Experience using research methods or other approaches relevant to the subject domain
• Work experience relevant to the proposed project
• Experience of presentation of research findings
• A demonstrable interest in or experience of using open science methods

Funding and eligibility

The University offers the following levels of support:

Vice Chancellors Research Studentship (VCRS)

The following scholarship options are available to applicants worldwide:

• Full Award: (full-time tuition fees + £19,000 (tbc))
• Part Award: (full-time tuition fees + £9,500)
• Fees Only Award: (full-time tuition fees)

These scholarships will cover full-time PhD tuition fees for three years (subject to satisfactory academic performance) and will provide a £900 per annum research training support grant (RTSG) to help support the PhD researcher.

Applicants who already hold a doctoral degree or who have been registered on a programme of research leading to the award of a doctoral degree on a full-time basis for more than one year (or part-time equivalent) are NOT eligible to apply for an award.

Please note: you will automatically be entered into the competition for the Full Award, unless you state otherwise in your application.

Department for the Economy (DFE)

The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £19,000 (tbc) per annum for three years (subject to satisfactory academic performance).

This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.

• Candidates with pre-settled or settled status under the EU Settlement Scheme, who also satisfy a three year residency requirement in the UK prior to the start of the course for which a Studentship is held MAY receive a Studentship covering fees and maintenance.
• Republic of Ireland (ROI) nationals who satisfy three years’ residency in the UK prior to the start of the course MAY receive a Studentship covering fees and maintenance (ROI nationals don’t need to have pre-settled or settled status under the EU Settlement Scheme to qualify).
• Other non-ROI EU applicants are ‘International’ are not eligible for this source of funding.
• Applicants who already hold a doctoral degree or who have been registered on a programme of research leading to the award of a doctoral degree on a full-time basis for more than one year (or part-time equivalent) are NOT eligible to apply for an award.

Due consideration should be given to financing your studies. Further information on cost of living