Pushing the frontiers of water quality management through the development and application of bacteriophage-based pollution diagnostic tools

This interdisciplinary project aims to develop a ground-breaking precision tool that identifies human faecal pollution in water, using DNA sequencing and bacteriophage (viruses that infect bacteria) as diagnostic indicators. This innovative approach addresses critical shortcomings of current culture-based methods by offering a rapid, accurate and sensitive tool that can identify human faecal pollution. The development of this technology is timely, given the increasing pressures on UK freshwater quality and the urgent need for better water quality monitoring and pollution control. Freshwater ecosystems in the UK are under significant strain, with only 16% of English rivers achieving “good ecological status,” and none meeting “good chemical status.” Key pollution sources include agricultural and urban runoff, as well as wastewater discharges, which pose risks to biodiversity and public health, e.g. via recreational water use or drinking water abstraction. At its core, the project seeks to apply and optimise bacteriophage-based pollution diagnostics. Bacteriophage are advantageous because they are highly abundant in faecal matter, persist longer in the environment than traditional bacterial indicators, and cannot replicate outside their hosts, making them reliable markers of contamination. The project’s first objective is to optimise the preparation of water samples and metagenome construction (i.e. process of collecting and combining all the genetic material from a sample, such as water, to create a complete picture of the microorganisms present) using portable Oxford Nanopore MinION™ sequencing technology, ensuring these processes are both accurate and efficient. The second objective focuses on identifying diagnostic bacteriophage-based ecogenomic signatures (unique patterns in the genetic material of organisms, that reflect their interactions with the environment) in metagenomic datasets and developing algorithms to accurately detect pollution. For the third objective, the newly developed diagnostic tool will be applied and tested on water samples from the River Wharfe, including its inland bathing site, in a blind pilot study to evaluate its effectiveness. Finally, the fourth objective is to work closely with stakeholders such as the Environment Agency, water companies, River Trusts, and community groups to shape the tool's development, assess its usability, and ensure the research findings are translated into practical outcomes through knowledge sharing, clear guidance, and widespread dissemination. The project builds on robust proof-of-concept data and the considerable expertise of the partner institutions. By advancing pollution diagnostics, this project will have far-reaching benefits. It will provide the Environment Agency (and other interested parties) with a more effective method for assessing water quality risks, including those in recreational and shellfish waters. It will support water companies in identifying pollution sources such as sewage spills and misconnections. The project’s results will contribute to improved ecological health, reduced public health risks, and enhanced recreational opportunities in freshwater systems. Ultimately, the diagnostic tool will represent a significant advancement towards safeguarding the UK’s water resources and addressing the pressing challenges of freshwater pollution.