Developing novel CRISPR–mediated detection systems to monitor aquatic disease and invasive species

Aquaculture is the fastest growing food production sector globally (FAO 2020). However, infectious diseases continue to pose a major challenge to sustainable farming. These same diseases, in combination with invasive species, also pose a fundamental obstacle to marine conservation efforts worldwide. For example, the restoration of European oyster reefs2 is impeded by both the parasite Bonamia and the invasive slipper limpet.

Safe and successful movement of animals to aquaculture and restoration sites requires early and sensitive detection of pathogens and regular monitoring. The systems currently available tend to be expensive, lack sufficient sensitivity, or require specific training; this impedes the scalability for the regular monitoring required. As such, there is potential for development of new, disruptive technology to revolutionise detection.

The international SARS-CoV2 pandemic has seen tremendous global collaborative efforts to improve existing disease detection methods e.g. STOPCovid3; a cost-effective, user-friendly test with rapid output at point-of-care. This technology uses CRISPR to detect RNA before visualisation of results on a lateral flow device. The inherent flexibility of CRISPR means that assays can be designed to detect DNA or RNA from any species allowing for identification of pathogens or invasive species from aquatic samples.

Throughout the course of their PhD, the successful applicant will develop CRISPR-based detection assays for aquaculture. These assays will be optimised in the lab against the gold standards of PCR and Nanopore sequencing, and ultimately be validated in situ at target aquaculture and restoration settings around the UK.

As part of a new and growing research group, the student will be expected to travel nationally and internationally and work effectively in laboratory and field settings. The student will have the opportunity to be trained in molecular biology and bioinformatics and to interact directly with the aquaculture industry as required for the success of the project.