Supervisory Team:  Professor Jason Snape (University of York), Dr Matt Bawn, (University of Newcastle), Dr John Wilkinson (University of York), Dr Jenni Hughes (UKWIR), Dr Isobel Stanton (UKCEH), Dr Susan Zappala (JNCC).

Project description: LIMIT-AMR will demonstrate that chemical-based limits for antimicrobials offer limited protection to the threat of antimicrobial resistance (AMR) and establish an integrated approach to address the risks that antibiotic and AMR exposure pose to public health and ecosystem services through treated effluents.

Current approaches to protect environmental and public health use environmental quality standards (EQSs) i.e. they provide an environmental concentration for that chemical that should not be exceeded in any discharge. LIMIT-AMR will demonstrate that EQSs for antimicrobials are not a silver bullet to manage AMR related risks because 

1. EQS limits are chemical specific and AMR is class-wide; 

2. resistance mechanisms for some antimicrobials are biodegradative (e.g. extended spectrum beta-lactamase activity) so the absence of the antibiotic does not equate to absence of resistance; and 

3. they do not consider co-selective pressures. 

LIMIT-AMR will combine microbiological, metagenomic profiling of resistance genes and mobile genetic elements (MGEs) using Oxford Nanopore sequencing, and analytical chemistry (high resolution LC-MS/MS) to explore the relationships between antimicrobial exposure and AMR within different WWTPs systems. Molecular data will interpret AMR not just as gene presence/absence, but in terms of genetic context (plasmids, integrons, transposons), persistence, and dissemination potential. LIMIT-AMR will focus antibiotics containing a beta-lactam ring where resistance is known to result in the cleavage of that ring. The presence of transformation products will be investigated that may indicate the presence of extended spectrum beta-lactamase activity as part of a more holistic and integrated approach to managing AMR. 

Student: James Mason

Supervisory Team: Dr Matthew Reilly (University of York), Dr Richard Daniel (University of Newcastle), Professor Jason Snape (University of York), Professor James Chong (University of York), Dr Des Devlin (Dŵr Cymru Welsh Water).

Project description: Recent public concern regarding the escape of pathogens like E. coli and Salmonella from Sewage Treatment Works (STW) into watercourses has intensified the scrutiny of sludge management. As the available landbank for biosolids decreases, regulatory standards for land-spreading are expected to become more stringent. Current pathogen monitoring relies on traditional culture-based plating, which is time-consuming and susceptible to interference from the complex, particulate nature of sewage solids.

Inaccurate monitoring poses a dual threat: significant environmental risk from undetected pathogens and massive operational costs from false positives. If digestate biosolids fail compliance, water companies often resort to transporting wastes between STWs, which increases carbon emissions and can cost tens of thousands of pounds. Resolution could also necessitate a full digester clean and restart, a task that can incur costs over £1M.

This project will seek a robust, molecular-based methodology for enumerating viable pathogens in processed biosolids. A critical component will be a comparative study of sludge interference, evaluating how the particulate nature of different matrices including limed, digested, and thermally hydrolysed sludges influence the accuracy of plating and molecular techniques.

The use of Propidium Monoazide (PMA)-multiplex qPCR will be developed and validated against typical plating methods. We aim to reduce measurement times from days to hours while increasing taxonomic resolution. A key focus will be developing a standardised "wash and resuspend" pre-treatment to ensure reliable DNA amplification and clearer plating results. We intend to provide a risk-scoring framework that differentiates between commensal and pathogenic strains, enhancing both regulatory compliance and operational efficiency.

Supervisory Team: Dr Matthew Brown (University of Newcastle), Professor James Chong (University of York), Tom Taylor (Yorkshire Water)

Project Description: Wastewater routinely harbours human-derived pathogens and can serve as a reservoir and conduit for antimicrobial-resistant bacteria (ARB) and resistance genes (ARGs), which may persist through conventional treatment and be released via effluents or biosolids. As populations grow and urbanise, and climate-driven extremes increasingly overwhelm sewer networks and treatment capacity, overflows and downstream exposure to waterborne disease and anti-microbial resistance (AMR) are likely to increase. While tertiary disinfection (UV, ozonation, chlorination) can reduce microbial loads, pathogen and ARB/ARG attenuation can be variable and entails significant energy and by-product trade-offs, underscoring the need for additional targeted, sustainable interventions to curb release.

Bacteriophages, viruses that infect bacteria, present a viable, sustainable and underexploited engineering solution. As nature’s precision weapons against bacteria, lytic phages prey on, replicate within, and ultimately lyse their hosts. Because this mechanism differs from that of antibiotics, phage “therapy”, i.e. the application of lytic phages to achieve bactericidal effects, represents an attractive treatment modality for ARB, and pathogens more broadly.

We will develop and validate bacteriophage-based strategies to selectively suppress pathogens and reduce AMR pressure in wastewater environments, using ESKAPE pathogens as exemplars. The project will (i) isolate and characterise lytic phages using conventional culture-based methods, next-generation isolation techniques and genome sequencing; (iii) engineer broad-range, resistance-resilient phage cocktails through rational screening, complemented with polyvalent phage isolation and/or host range expansion; and (iv) test deployment in tertiary treatment at Newcastle’s BEWISe facility, including phage-augmented constructed wetlands as nature-based barriers to pathogen/ARB/ARG release, with parallel evaluation of phage application to sludge-derived biosolids/digestate.

Supervisory Team: Professor Michael Plevin (University of York), Dr Akane Kawamura University of Newcastle), Dr Mark Craig (Severn Trent), Professor Steve Johnston (University of York).

Project Description: The public use UK waterways and beaches for a variety of leisure activities, however in almost all cases real-time up-to-date knowledge of whether the water is safe to use and free from pathogens is unavailable. This project aims to generate highly sensitive, low-cost, portable biosensing technologies that can provide point-of-use information about pathogen levels thereby allowing the public to better determine the health risks of bathing.

We have developed a novel class of synthetic protein scaffold that shows remarkable resilience to chemical and environmental challenges. The scaffold can be engineered to function as a protein bioreceptor that can be coupled to biosensors to detect analytes, offering a new alternative to antibodies or aptamers. Moreover, the scaffold shows strong antifouling capacity, meaning our protein technology introduces multiple favourable properties in biosensor design. In this project, we will design and engineer protein bioreceptors that bind microbial and viral targets that are either pathogens themselves or indicators of water contamination. We will partner with companies specialising in lower-cost sensing technologies to develop protein-based sensors that can be used in the field by the general public. The design and engineering context will be set via collaboration with Severn Trent Water and other water companies, who will also provide access to relevant samples, technologies and infrastructure. As well as empowering public users of UK waterways and beaches, biosensors for pathogen detection will enhance the ability of water companies to more rapidly and frequently monitor the presence of pathogens in waterways and water processing facilities. 

Supervisory Team: Dr Matt Bawn (University of Newcastle), Professor Gavin Thomas (University of Newcastle), Dr Jenni Hughes (UKWIR), Dr Mark Bruce (Oxford Nanopore Technology).

Project Description: Wastewater treatment systems rely on complex microbial communities structured as biofilms and flocculated aggregates to remove contaminants and protect public and environmental health. However, most current genomic approaches average signals across populations, masking fine-scale diversity that underpins adaptation, resilience, antimicrobial resistance (AMR), and pathogen persistence. This project aims to develop and apply single-cell whole-genome sequencing (WGS) using Oxford Nanopore technologies to resolve microbial population diversity within wastewater-associated biofilms and provide ground-truth validation of microbial community structure in engineered systems.

Metagenomic sequencing will be applied across wastewater treatment systems to establish a baseline overview of microbial diversity, functional potential, and seasonal variation. This will identify priority taxa, biofilm niches, and environmental drivers while generating an industry-relevant reference dataset for benchmarking treatment performance.

Environment-informed in vitro biofilm communities will be developed, seeded from wastewater-derived populations and grown under treatment-relevant conditions. These systems will be used to develop and validate single-cell nanopore WGS workflows, including cell separation, whole-genome amplification, sequencing, and bioinformatic quality control. Benchmarking against defined communities will quantify bias, coverage, and reproducibility.

Validated pipelines will be applied directly to wastewater biofilms, enabling resolution of within-population genomic variation, mobile genetic elements, and AMR context not accessible via bulk metagenomics. This will enable detection of rare variants and emergent lineages, providing capability to investigate “unknown unknowns” in microbial communities and improving confidence in genomic surveillance approaches. Together, this project delivers a scalable framework for high-resolution microbial ground-truthing and surveillance in engineered water systems. 

Student: Jess Hatton

Supervisory Team: Professor Tom Curtis (University of Newcastle), Dr Sarah Forrester (University of York), Dr Chris Jones (Northumbrian Water Group), Dr David Baidock (Southwest Water), Dr Martin Spurr (Environment Agency)

Project Description: Nationally and globally the water industry spends billions of pounds on infrastructure to protect customers from microbial risks. The focus in the UK is on recreational waters. However, in the foreseeable future water reuse, especially in agriculture, will become common place in the UK.

That investment, the health of our citizens and the trust in the water system rests on our understanding and assessment of the microbial risk.

However, our assessment of that risk is built on science and studies that are outdated. In essence our assessment of the risk to recreational water users is based on empirical relationships between the concentration of certain culturable faecal indicator organisms (1950s technology) and the risk to a swimmer in a (determined in the 1980s) very restricted setting. It is time for a rethink.

The foundation for that rethink will be the use of modern molecular tools to directly and authoritatively determine the hazard, pathogenic virus concentrations, fate and ecology. The recent development of capsid integrity quantitative PCR (CI-qPCR) is presenting us with an opportunity. There is no doubt the method works in principle.

The challenge for this research project will be to develop suitable concentration protocols (using large volume filtration), determine which viruses are most abundant in UK surface and recreational waters, where possible validate that finding using tissue culture and determine the rate and mechanisms of decay in recreational, and to incorporate those findings in transport models. This will lay the foundation for new assessments of risk grounded in models or epidemiology.

Student: Fergal Buckley 

Supervisory Team: Dr Matthew Reilly (University of York), Professor Russell Davenport (University of Newcastle), Professor James Chong (University of York), Dr Tom Taylor (Yorkshire Water)

Project Description: The UK produces 11 billion litres of wastewater every day and treatment contributes to around 2-3% of national electricity demand. Conventional processing is dominated by the exploitation of microorganisms growing in energy-intensive aeration lanes. Aeration lanes receive oxygen from air blowers, which account for 50-70% of a site's electricity use and drive the release of nitrous oxide (N2O), a greenhouse gas approximately 300 times more potent than CO2. Hence, there is an urgent need for innovative, low-cost, and sustainable wastewater treatment solutions.

While most conventional systems rely on aerobic processes, alternative anaerobic approaches offer a promising route toward lower energy use and reduced emissions. An upflow anaerobic sludge blanket (UASB) is a high-rate anaerobic treatment reactor. In a UASB, wastewater flows upward through a dense blanket of microbial granules which remove organic matter. UASBs have the potential to omit the need for blowers, avoid the release of N2O and generate green biogas fuel. Furthermore, exploitation of anaerobic microbiology enables production of volatile fatty acids (VFAs) which have potential for use as green industrial chemical feedstocks to produce high value products such as polymers, adhesives, and solvents.

This project will test bench-scale multi-stage UASB reactors, comparing single- and two-stage systems for pollutant removal, pathogen destruction, biogas generation, and VFA yields. It will dive into microbial community characterisation using DNA sequencing to interrogate the biology driving system performance.