Fieldwork

Our environmental surveillance activities began in 2010 with research on viral dynamics in the Conwy River and estuary, responding to local water quality concerns. This early work, supported by the UK Natural Environment Research Council (NERC), was subsequently expanded to rivers and estuaries across Wales and England, with funding from the water industry, Welsh Government, Environment Agency and the Food Standards Agency.

In 2020, we received funding from the Department for Environment Food and Rural Affairs and Department of Health and Social Care to establish a high-throughput laboratory, which became one of only two national wastewater-based epidemiology (WBE) laboratories supporting the UK’s COVID-19 surveillance programme. Working in partnership with the Environment Agency, we delivered the English WBE programme for COVID-19 surveillance. Since 2021, we have led the Wales WBE programme, monitoring wastewater from treatment works nationwide multiple times per week. These analyses encompass a broad range of biological and chemical indicators, including antimicrobial resistance (AMR) genes, viruses, fungi, microplastics, and priority chemical contaminants.

In parallel, we led the Wales component of the PathSafe project, investigating the environmental impacts of hospital wastewater, and contributed to the EU Horizon BlueAdapt project, which examines the movement of AMR and viral pathogens in coastal environments. Together, these programmes underpin our integrated, One Health approach to understanding the fate, transport, and risks associated with enteric pathogens and AMR in environmental systems. To address these challenges, our fieldwork objectives include:

1. Evaluating Methods for Pathogen Recovery 

We routinely collect representative wastewater, freshwater, marine water, and sediment samples from wastewater treatment works, rivers, estuaries, and coastal environments. These samples are used in controlled laboratory experiments in which known concentrations of target microbial pathogens, including viruses (e.g. SARS-CoV-2, norovirus, influenza) and antimicrobial resistance (AMR)-carrying bacteria, are introduced. This approach allows us to systematically compare and optimise pathogen recovery and detection techniques, supporting the development of robust, standardised protocols for environmental surveillance. In parallel, we assess the persistence and behaviour of AMR genes and mobile genetic elements across different environmental matrices.

2. Assessing the Efficiency of Wastewater Treatment on Pathogen Removal 

We investigate how microbial pathogens and antimicrobial resistance (AMR) attenuate, persist, or transform as wastewater moves through sewer networks and undergoes treatment. Using a combination of molecular methods (including RT-qPCR) and infectivity assays, we estimate pathogen viability and quantify the discharge of treated effluent into the environment. To capture changes in pathogen composition and evolution, we apply both long-read (Oxford Nanopore Technologies) and short-read (Illumina) sequencing, including tiled amplicon, amplicon, and metagenomic approaches, to characterise shifts in pathogen diversity and AMR profiles across treatment stages. This work also includes tracking pathogen surrogates (e.g. bacteriophage tracers) and clinically relevant targets such as SARS-CoV-2, alongside the use of fluorescent tracers (e.g. Rhodamine) and in situ sensor arrays (e.g. fluorescence, turbidity, electrical conductivity, and pH) to quantify wastewater transit times across sewersheds and treatment systems.

3. Exploring Viral and AMR Movement in the Environment 

We regularly sample surface water, wastewater, sediment, and shellfish at rivers, estuaries, and major treatment plants across England and Wales. Using RT-qPCR and dd-PCR, we measure viral and AMR concentrations, followed by metagenomic and infectivity analyses to assess human exposure risks. These samples help us understand the seasonal and spatial dynamics of these organisms, and their results inform our viral and AMR transport models, and aid risk assessments for recreational waters, beaches, and shellfish beds. 

4. Evaluating Viral and AMR Diversity Over Time 

We use high-throughput sequencing tools (Illumina NextSeq, Oxford Nanopore MinION and GridION) to sequence viruses and analyse the abundance and diversity of antimicrobial resistance genes in our samples. During the COVID-19 pandemic, these techniques helped detect new SARS-CoV-2 variants and are now being used to track the diversity of other viruses such as influenza and norovirus. Our findings have been integral in informing government policies, such as evidenced by the First Minister of Wales, Eluned Morgan, at the recent Wales COVID-19 Inquiry.

5. Our Approaches for Pathogen and Contaminant Monitoring 

We deploy a range of complementary sampling approaches to monitor viral, microbial, and antimicrobial resistance (AMR) dynamics over time. These include:

• Automated, refrigerated composite samplers for high-frequency collection supporting pathogen, nutrient and contaminant analyses.

• Passive samplers for the in-situ concentration of chemical contaminants from wastewater and environmental waters.

• Novel biological passive samplers, using tailored enrichment matrices to capture viruses and bacteria, providing time-integrated signals over several days.

Together, these tools are used to investigate temporal variability within sewer networks (including near-source monitoring) and to quantify diurnal discharge patterns from wastewater treatment works, as well as fluctuations in environmental waters.