This document was created as part of the H2020 All Atlantic Ocean Sustainable, Profitable and Resilient Aquaculture (ASTRAL) project. The aim of this deliverable is to describe the main microbial pathogens that are capable of severely affecting productivity in each of the ASTRAL IMTA Labs, describe the current detection methods in aquaculture facilities and identify emerging technologies to improve early warning systems.

To contextualize the main pathogen issues in each IMTA lab, several directives and categorizations of fish health status and pathogen risks were identified and summarized. Subsequently, key pathogens for the aquaculture industry, and the current diagnostics used to detect them, were described based on an extensive literature review and the experience of each IMTA lab. Moreover, identified pathogens and bacterial diversity were provided for land-based IMTA labs located in Brazil and South Africa. Finally, molecular tools, biosensors and predictive models were proposed to improve current monitoring methods of the main species-specific pathogens described in the first part of the deliverable. 

The results obtained will be useful to i) be aware of the directives that apply to the health status of cultured organisms in each IMTA laboratory depending on the country; ii) understand which potential pathogens can occur in each geographic region or IMTA system type and the environmental stressors linked to their infections; and iii) find innovative forms of monitoring using new and emerging technologies to tackle pathogens within the system anticipating potential outbreaks.