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Resistant rivers: can antimicrobial resistance spread through river networks?

NERC Doctoral Training Centre Studentships with CENTA

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Dr J U Kreft , Dr J Larsen , Prof E M H Wellington , Assoc Prof C Quince No more applications being accepted Competition Funded PhD Project (Students Worldwide)
Birmingham United Kingdom Ecotoxicology Hydrology Microbiology

About the Project

The widespread use of antibiotics in humans and animals has not only selected for resistance genes but also for plasmids carrying them. This has led to a growing global concern for the spread of antimicrobial resistance (AMR), which would have enormous public health implications for nations of all income and development levels. This project would enable the student to gain inter-disciplinary training and mentoring to tackle a largely unknown but critical link in the spread of AMR, namely if and to what extent AMR can persist in our river networks. The student would have a range of options in river systems to explore, from new collaborations in India to the Thames in the UK, this project will provide the first assessment of how and when AMR can enter, persist, and be transported, within river systems with different pollution sources.

Resistance genes can enter the environment via hotspots such as hospital sewers, wastewater treatment plants and animal manures and slurries on farms. Runoff from these fields and effluent from wastewater treatment enter rivers and interact with river sediments. In addition, large rainfall and runoff events can overwhelm storm drainage and wastewater treatment systems, allowing untreated sewage to enter river systems directly.

Building on previous work, this project will develop a mechanistic mathematical model to better understand resistance selection and transport from wastewater, wastewater treatment to where effluent enters the river network, within the river itself, and its downstream transport. Importantly, this model will be placed in context of the hydrological functioning of the Thames catchment, and also incorporate the large metagenomic sequencing and antibiotic concentration datasets available throughout the catchment. Depending on the background and interests of the student, experimental studies of selection under low concentrations of antibiotics to validate the mathematical model can be included.

How to apply

Applications need to be submitted via the University of Birmingham postgraduate portal by midnight on 11.01.2021. Please first check whether the primary supervisor is within Geography, Earth and Environmental Sciences, or in Biosciences, and click on the corresponding PhD program on the application page.

This application should include

• a brief cover letter, CV, and the contact details for at least two referees

• a CENTA application form

• the supervisor and title of the project you are applying for under the Research Information section of the application form.

Referee’s will be invited to submit their references once you submit your application, but we strongly encourage applicants to ensure referees are aware of your submission and expecting a reference request from us. Students are also encouraged to visit and explore the additional information available on the CENTA website.


Hassoun-Kheir N, Stabholtz Y, Kreft JU, de la Cruz R, Romalde JL, Nesme J, Sørensen SJ, Smets BF, Graham D, Paul M (2020). Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review. Science of The Total Environment 743: 140804
Arya S, Todman H, Baker M, Hooton S, Millard A, Kreft JU, Hobman JL, Stekel DJ (2020). A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer. FEMS Microbiology Ecology 96: fiaa100
Hellweger FL, Clegg RJ, Clark JR, Plugge CM, Kreft JU (2016). Advancing microbial sciences by individual-based modelling. Nature Reviews Microbiology 14: 461–471
Amos GCA, Hawkey PM, Gaze WH, Wellington EM (2014). Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment. The Journal of Antimicrobial Chemotherapy 69: 1785–1791
Amos GCA, Zhang L, Hawkey PM, Gaze WH, Wellington EM (2014). Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes. Veterinary Microbiology 171: 441–447
Amos GCA, Gozzard E, Carter CE, Mead A, Bowes MJ, Hawkey PM, Zhang L, Singer AC, Gaze WH, Wellington EMH (2015). Validated predictive modelling of the environmental resistome. ISME Journal 9: 1467–1476
Lehmann K, Bell T, Bowes MJ, Amos GCA, Gaze WH, Wellington EMH, Singer AC (2016). Trace levels of sewage effluent are sufficient to increase class 1 integron prevalence in freshwater biofilms without changing the core community. Water Research 106: 163–170
Singer AC, Shaw H, Rhodes V, Hart A (2016). Review of Antimicrobial Resistance in the Environment and Its Relevance to Environmental Regulators. Frontiers in Microbiology 7: 1728

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