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Jennifer Shelton

Scientist, crafter & beekeeper

About Me

I'm currently a third year PhD student researching the fungus Aspergillus fumigatus, which plays an important role in the environment recycling nutrients from rotting plant material back into the soil. Unlike most bacteria and fungi, A. fumigatus enjoys growing at warm temperatures and can therefore be pathogenic to humans when we inhale its spores. It causes a number of illnesses, called aspergillosis, ranging from severe hypersensitisation and "fungal asthma", to chronic colonisation of the airways, to invasive bloodstream disease. Chronic and invasive aspergillosis result when our innate immune system fails to clear the spores we inhale, which then establish and grow in lung cavities.

The spores are tiny and lightweight and are carried on air currents - they are found indoors and outdoors, in the air and in the soil, and on every continent except for Antartica - and is estimated we inhale 100s of these spores every day.

Aspergillosis is treated with drugs containing azoles and A. fumigatus can develop resistance to azoles after long-term treatment. With increasing frequency individuals who have never been treated with azole drugs are presenting with infections that are azole-resistant, which suggests that the spores had acquired resistance before they'd inhaled them. It is now widely believed that spores circulating in the environment acquire azole-resistance from exposure to agriculture fungicides containing azoles with a similar structure to medical azoles.

This is where my PhD comes in! To test this, and to determine the background level of azole-resistant spores circulating in the UK, I organised two citizen science projects. The first project #ScienceSolstice asked volunteers to collect air samples from their homes and workplaces on solstice and equinox dates between June 2018 and March 2019. The second project #SummerSoilstice asked volunteers to collect a soil sample from their garden on summer solstice 2019. From these samples I cultured A. fumigatus and tested each isolate for resistance to tebuconazole - the third most-sprayed azole in fungicides here in the UK.

In my final year I will be sequencing the gene region of A. fumigatus that is responsible for azole-resistance to determine which mutations have occurred in my isolates, and investigating whether these are linked to factors such as seasonality or land use.

My supervisors are Professor Matthew Fisher at Imperial College London and Dr Andrew Singer at UK Centre for Ecology & Hydrology.


Before starting my PhD I worked in Mat Fisher's group as a Research Assistant researching the impact of amphibian skin mycobiome on infection with the fungal pathogen Batrachochytrium dendrobatidis. (2015-2017)

Prior to this, I worked as a Data Analyst for MalariaGEN researching the genetic determinants of acquired immunity to malaria. (2012-2015)

I completed my MSc in Epidemiology, specialising in infectious diseases, at Imperial College London with a dissertation investigating the likelihood of serotype replacement following vaccination against human papillomavirus. (2011-2012)

My undergraduate degree was in Biomedical Science from University of Warwick and my dissertation focussed on the effect of foot conformation on footrot and treatment for lameness in sheep.



I have received several prizes for posters and talks presented at conferences during my PhD.

In 2016 I was awarded a National Geographic Young Explorer's Grant to investigate ancient assocations between amphibians and chytrid fungi in Taiwan.


I really enjoy talking to people about my research, and about science in general, and have given talks and held stands at several science events. Some examples include:

"#ScienceSolstice: when mycology meets citizen science" - talk for adults at Cafe Scientifique popular science events.

"Fungi: the good, the bad and the ugly" - talk for school-aged children in science lessons or at STEM events.

"Fungal Hunters" - stand at Imperial Lates event with fungal DNA trail map.

If you'd like me to give a talk about fungi or my citizen science projects to your school, workplace or interest group please email me at [email protected]


Shelton, J.M.G., Fisher, M.C. and Singer, A.C. (2020): Campaign-Based Citizen Science for Environmental Mycology: The Science Solstice and Summer Soil-Stice Projects to Assess Drug Resistance in Air- and Soil-Borne Aspergillus fumigatus. Citizen Science: Theory and Practice, 5(1), 1-13.

Malaria Genomic Epidemiology Network. (2019): Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. Nature Communications 10(5732), 1-19.

Bates, K., Shelton, J., Mercier, V., Hopkins, K., Harrison, X., Petrovan, S., Fisher, M. (2019): Captivity and infection by the fungal pathogen Batrachochytrium salamandrivorans perturb the amphibian skin microbiome. Frontiers in Microbiology 10, 1834.

Sewell, T., Zhang, Y., Brackin, A., Shelton, J., Rhodes, J., Fisher, M. (2019): Elevated prevalence of azole resistant Aspergillus fumigatus in urban versus rural environments in the United Kingdom. Antimicrobial Agents and Chemotherapy.

Beukema, W., Martel, A., Nguyen, T., Goka, K., Schmeller, D., et al. (2018): Environmental context and differences between native and invasive observed niches of Batrachochytrium salamandrivorans affect invasion risk assessments in the Western Palaearctic. Diversity and Distributions 24(12), 1788-1801.

Fisher, M., Ghosh, P., Shelton, J., Bates, K., Brookes, L., Wierzbicki, C., Rosa, G., et al. (2018): Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi. Scientific Reports 8(1), 7772.

O’Hanlon, S., Rieuz, A., Farrer, R., Rosa, G., Waldman, B., Bataille, A., Kosch, T., et al. (2018): Recent Asian origin of chytrid fungi causing global amphibian declines. Science 360(6389), 621-627.

Nash, A., Sewell, T., Farrer, R., Abdolrasouli, A., Shelton, J., Fisher, M., Rhodes, J. (2018) MARDy: Mycology Antifungal Resistance Database. Bioinformatics 34(18), 3233-3234.

Cunningham, A., Beckmann, K., Perkins, M., Fitzpatrick, L., Comie, R., Redbond, J., O’Brien, M., Ghosh, P., Shelton, J., Fisher, M. (2015): Emerging disease in UK amphibians. Veterinary Record 176(18), 468.

Shelton, J., et al. in collaboration with MalariaGEN Consortium. (2015) Genetic determinants of anti-malarial acquired immunity in a large multi-centre study. Malaria Journal 14(1),333.

Shelton, J., Usherwood, N., Wapenaar, W., Brennan, M., Green, L. (2012): Measurement and error of hoof horn growth rate in sheep. The Journal of Agricultural Science 150(3), 373-378.