The Future of Pathogen Detection in Aquaculture: Miniature Labs, Field‐Compatible Assays, environmental DNA and RNA, CRISPR and Metatranscriptomics

Inland recirculating aquaculture is a thriving food industry providing sustainable and locally sourced high-quality protein. However, its expansion is accompanied by emerging challenges regarding the spread of pathogens and diseases. Detection and management of pathogens in aquaculture remain underdeveloped compared to other animal farming sectors due to the vast diversity of species involved, the non-domesticated species and limited knowledge regarding pathogens, host responses and disease mechanisms. Furthermore, recirculating aquaculture systems are heavily dependent on beneficial bacterial communities for waste product removal and water quality maintenance, with opportunistic pathogens constituting an inherent component of these microbial communities. To enhance the potential of inland aquaculture as a sustainable source of protein, it is imperative to adopt advanced tools for pathogen detection and monitoring and for assessing the overall health of the microbial ecosystem. This paper presents an overview of promising current molecular and technological advancements that offer solutions for pathogen detection and system monitoring in aquaculture. We focus on recently developed point-of-care and on-site detection methods using miniaturized laboratory equipment and robust workflows that operate independently of cold chain logistics. We explore current methodologies for monitoring pathogens in the environment rather than through fish health assessments. Lastly, we discuss techniques from other scientific disciplines in aquaculture, including CRISPR-Cas protocols for pathogen detection and the implementation of ‘omics’ approaches for the comprehensive characterization of microbial states. These methods demonstrate considerable potential for pathogen surveillance and, subsequently, early responses in the dynamic aquaculture field. Through a better understanding of available options, aquaculture managers and molecular scientists can collaborate and optimize systems. This paper aims to facilitate communication between molecular scientists and aquaculture managers, equipping the aquaculture industry with knowledge to enhance pathogen management techniques in their facilities.