High‐Throughput Sequencing in Aquaculture Disease Investigations: Challenges and Opportunities for Implementation

ABSTRACT The current generation of sequencing technologies can produce terabases of data with exceptional accuracy and speed, at a fraction of the cost of older methods. Despite this unprecedented power, adoption into aquaculture health management presents several challenges, including identifying where such capability may be optimally deployed. Here we synthesise discussions from a structured expert workshop held at the 2025 Aotearoa Aquatic Diseases Symposium in Dunedin, New Zealand, where experts from industry, government and academia explored the challenges and opportunities for adopting high‐throughput sequencing (HTS) to support disease investigations in aquaculture. Workshop participants identified key applications for HTS, including pathogen discovery during unexplained mortality events and source attribution in epidemics, but also noted technical, regulatory and social challenges for widespread adoption. These include the need for standardised sampling and bioinformatic workflows, data sovereignty, equitable access to the technology and uncertainty around interpreting detection of notifiable pathogens. Targeted research and coordinated regulatory frameworks will be essential to guide responsible use of HTS and determine where it adds value relative to existing approaches. Clarifying these opportunities and constraints will guide the responsible adoption of HTS into aquaculture health management to support sustainable growth for the sector.