Citizen science approaches to environmental sampling for AMR: #ScienceSolstice and #SummerSolstice

© iStock/pariwat pannium

The Microbiology Society is undertaking a project entitled A Sustainable Future as part of our 75th Anniversary, which aims to highlight the Sustainable Development Goals (SDGs) to our members and empower them to use their research to evidence and impact the goals. Earlier this year, we put a call out to our members to submit case studies in the following three areas: antimicrobial resistance, soil health and the circular economy.

This case study is written by Jennifer Shelton, who is a final year PhD student at Imperial College London. It focuses on antimicrobial resistance; a naturally occurring process, whereby micro-organisms (bacteria, viruses, fungi and parasites) can change and adapt over time, either by modifying the target of the antimicrobial, or by developing and exchanging resistance genes.

What are the challenges/needs that this research/initiative addresses?

Aspergillus fumigatus is a ubiquitous fungus: it is in the air and in the soil and can be found on every continent except Antarctica. It plays an important role in soil, recycling nutrients from decaying organic matter, and produces tiny lightweight spores that can be carried on air currents. As a result, it is estimated that we each inhale several hundred A. fumigatus spores every day [1], which can trigger a severe allergic response or asthma. A. fumigatus is unusual, in that it loves to grow at 37oC – human body temperature – so if the spores are not cleared by an individual’s innate immune response once inhaled, they can lodge in the sinuses or lung cavities and grow, resulting in chronic aspergillosis infection. These infections occur most often in immunocompromised individuals - those receiving immunosuppressant drugs, undergoing chemotherapy or suffering from HIV/AIDS - but can also affect heavy smokers, COPD patients or follow on from influenza, COVID-19 or tuberculosis infections. If the fungus spreads from the respiratory tract into the bloodstream it causes invasive aspergillosis, which has a fatality rate ranging from 30-90% [2]. Aspergillosis is treated with drugs containing azoles, which are similar in structure to those sprayed on agricultural crops to protect against fungal plant pathogens. As a result, aspergillosis patients who have not been previously treated with azoles are presenting with azole-resistant infections, which implies the spores acquired resistance from the environment before they were inhaled.

To test this, I ran two citizen science projects #ScienceSolstice and #SummerSoilstice asking volunteers to collect air and soil samples, respectively, on five solstice and equinox dates between June 2018 and June 2019. The air samples were collected by placing adhesive films on outside ground floor windowsills and exposing them for 6-10 hours and soil samples were collected from borders, pots and compost heaps in back gardens, and were posted to me in the lab for growing Aspergillus fumigatus. All isolates grown were then tested for azole-resistance.

© Jennifer Shelton

Posters shared on social media platforms and displayed on noticeboards at Imperial College London and UK Centre for Ecology & Hydrology to recruit volunteers for the #ScienceSolstice and #SummerSoilstice citizen science projects.

What findings and solutions were provided by this research/initiative?

These projects aimed to determine the proportion of A. fumigatus spores in the UK environment that are azole-resistant, with a focus on residential areas. This is as opposed to sampling from farmland or industrial composting sites that are thought to be driving the development of resistance, but does not explain the exposure of members of the public to azole-resistant spores as they go about their everyday lives.

The projects were a great success and 787 volunteers from all over the UK took part on one or more of the sampling dates. Together they collected 2,132 air samples and 509 soil sampling that, combined, grew 7,991 A. fumigatus isolates [3]. This is the largest number of isolates collected by a single study to date and will provide valuable insight into the distribution of azole-resistant spores across the UK, and the potential public health threat they pose.

© Jennifer Shelton

Figure 2: A) Multiple Aspergillus fumigatus colonies growing on an agar plate. B)  A. fumigatus under the microscope at x400 magnification. 

What is the future for research and innovation in this area?

All isolates able to grow in the presence of azoles will have their DNA sequenced to determine the mutations responsible for resistance. As air samples were collected on single timepoints in each season throughout the year, it may be possible to detect an effect of seasonality (a proxy for temperature, humidity and farming practices) on numbers of circulating spores or proportion that are azole-resistant. Furthermore, knowing the location that spores were collected from will allow me to determine whether there is an association between surrounding land use types (for airborne spores) or garden soil location (for soilborne spores) and development of azole-resistance.

Aside from the importance of the data collected by these projects, and the implications of potential widespread antifungal resistance for farming practices and public health, an unexpected outcome was the level of engagement by citizen scientists. The number and geographical distribution of environmental samples collected throughout the year could not have been achieved without their participation, and the huge number of spores cultured shows the validity of a citizen approach for mycological data collection. Volunteers were enthusiastic, supportive and interested to know results, and I have happily given talks at school, popular science events and conferences at the request of participants. Furthermore, aspergillosis suffers from a lack of awareness and understanding, and I believe these citizen science projects have allowed me engage a greater audience about these diseases and to promote the work of The Aspergillosis Trust, which is a support group for patients and their families. I am incredibly grateful to all those who took part in the projects and would urge other mycologists and microbiologists to consider involving the public in their research too.


[1]        T. M. Hohl and M. Feldmesser, “Aspergillus fumigatus: Principles of pathogenesis and host defense,” Eukaryot. Cell, vol. 6, no. 11, pp. 1953–1963, 2007.

[2]        A. A. Brakhage and K. Langfelder, “Menacing Mold: The Molecular Biology of Aspergillus fumigatus,” Annu. Rev. Microbiol., vol. 56, pp. 433–455, 2002.

[3]        J. M. G. Shelton, M. C. Fisher, and A. C. Singer, “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,” Citiz. Sci. Theory Pract., vol. 5, no. 1, p. 20, 2020.

About the author

Jennifer Shelton is a final year PhD student on the Science and Solutions for a Changing Planet DTP, supervised by Professor Matthew Fisher at Imperial College London and Dr Andrew Singer at UK Centre for Ecology and Hydrology. Her PhD focuses on looking at the environmental drivers of AMR in Aspergillus fumigatus and its implications for human health.