Antimicrobial resistance (AMR) is a growing global health threat. By 2050, it is projected to become the leading cause of death worldwide. Among the contributors to this crisis are fungi, which cause a wide range of diseases. Further, environmental fungi are known to cause serious infections in immunocompromised individuals. A notable example is Aspergillus fumigatus, a common environmental fungus found in soil and decaying organic matter. Infections caused by A. fumigatus can lead to aspergillosis, a disease that becomes significantly more lethal when the fungal strain is resistant to clinical antifungal treatment. Despite this risk, azoles are used as plant protection products, which has the potential to increase azole resistance in A. fumigatus, meaning that this opportunistic pathogen may be cross-resistant to clinical azoles. This increases the risk of future treatment failures in the clinic.
Whilst there is a growing body of research into understanding concentrations that select for resistance in bacteria, this is currently lacking in fungi. This represents a critical knowledge gap for achieving satisfactory risk characterisation and assessments of environments in which azole-fungicides are found (e.g., agriculture, composters, waste- and runoff water).
In this PhD project, we aim to determine the minimal selective concentration (MSC) of agricultural azole fungicides, i.e., the lowest concentration at which resistant fungal strains are enriched over susceptible strains, in real-world substrates such as compost. This project will also investigate the bioavailability of fungicides to A. fumigatus across different stages of decay, as bioavailability may significantly alter the risk of resistance emergence. The studentship seeks to define what a “hotspot” looks like, i.e., locations where the concentration of azole-fungicide is sufficiently high to select for resistance in A. fumigatus. Filling this knowledge gap will enable the development of environmentally sustainable agricultural and composting practices aimed at limiting antifungal resistance selection, and, ultimately, protecting the efficacy of clinical antifungals, leading to better human health outcomes.
This project is a CENTA Flagship Project.
This project is not suitable for CASE funding
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This PhD project will investigate selection for antifungal resistance in Aspergillus fumigatus by undertaking laboratory-scale experiments. It will also investigate dynamics of antifungal bioavailability on the risk of selection developing. This work will investigate selection potential in a controlled manner using both liquid experiments, where antifungals are fully bioavailable and artificial compost, where bioavailability will be limited by the partitioning coefficient of each azole fungicide under study. Further, experiments with single strains of A. fumigatus will be undertaken, as well as exploring the dynamics of mixed environmental fungal communities. The student will learn classical microbiological techniques, as well as DNA-based skills in the UKCEH molecular laboratories. In addition, they will use statistical and bioinformatic analyses to interpret their findings.
DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.
The successful candidate will be based at the UK Centre for Ecology & Hydrology within the Molecular Ecology group. They will receive training in microbiology culturing, including in our dedicated fungal laboratory. Further, they will gain skills in molecular techniques, such as PCR and sequencing. In addition, they will be trained in analysing laboratory assay results, including the use of bioinformatics tools and statistical analyses. In addition, experience will be provided by working with the co-supervisors on translating outcomes into technical guidance for industry to better understand, manage and communicate the potential hazards and risks to improve real world assessments.
The Chief Scientist’s Group leads on science and research for the Environment Agency. We work across the organisation to consolidate, interpret and communicate evidence needed to protect health and the environment through our regulatory role. We will provide in-kind support as co-supervisor, including advice and guidance to help provide impact in real world applications.
Professor Matthew Fisher, Imperial College London, is an expert in the field of emerging pathogenic fungi. He will provide in-kind supper as co-supervisor, including advice and guidance to the student on the detailed fungal science and theory required to conduct this research.
Year 1: Literature review and laboratory scale undertaking single strain competition experiments in media.
Year 2: Laboratory scale experiments to understand bioavailability of fungicides in artificial compost using single strain competition experiments.
Year 3: Laboratory scale experiments using mixed communities in compost and write up of doctoral thesis.
ENVIRONMENT AGENCY 2024. Determining selective concentrations for antibiotics and antifungals in natural environments.
FISHER, M. C., BURNETT, F., CHANDLER, C., GOW, N. A. R., GURR, S., HART, A., HOLMES, A., MAY, R. C., QUINN, J., SOLIMAN, T., TALBOT, N. J., WEST, H. M., WEST, J. S., WHITE, P. L., BROMLEY, M. & ARMSTRONG-JAMES, D. 2024. A one health roadmap towards understanding and mitigating emerging Fungal Antimicrobial Resistance: fAMR. NPJ Antimicrob Resist, 2, 36.
MURRAY, A. K., STANTON, I. C., TIPPER, H. J., WILKINSON, H., SCHMIDT, W., HART, A., SINGER, A. C. & GAZE, W. H. 2024. A critical meta-analysis of predicted no effect concentrations for antimicrobial resistance selection in the environment. Water Res, 266, 122310.
SCHOUSTRA, S. E., ZHANG, J., ZWAAN, B. J., DEBETS, A. J. F., VERWEIJ, P., BUIJTENHUIJS, D. & RIETVELD, A. G. 2019. New insights in the development of azole-resistance in Aspergillus fumigatus. RIVM official reports.
STANTON, I. C., MURRAY, A. K., ZHANG, L., SNAPE, J. & GAZE, W. H. 2020. Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration. Commun Biol, 3, 467.
This project will follow on from research led by Imperial College London, with the UK Centre for Ecology & Hydrology, The Open University, as well as National Institute of Agricultural Botany as part of the NERC Highlight Topic grant “Monitoring for azole-resistant Aspergillus fumigatus”: Monitoring for azole-resistant Aspergillus fumigatus (MARAf) | UK Centre for Ecology & Hydrology. Further, it will follow a successful collaboration between the Environment Agency’s Chief Scientist’s group and the UK Centre for Ecology & Hydrology, modelling selective concentrations of antifungals in aquatic and soil environments: Determining selective concentrations for antibiotics and antifungals in natural environments – GOV.UK
For any enquiries related to this project please contact Isobel Stanton, [email protected].
The successful applicant would be registered at The Open University.
To apply to this project:
Applications must be submitted by 23:59 GMT on Wednesday 7th January 2026.