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.

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Publication Details

Journal
Reviews in Aquaculture
Published
2026-07-28
DOI
https://doi.org/10.1111/raq.70193
Primary Topic
Myxozoan Parasites in Aquatic Species
Type
article
Field-Weighted Citation Impact
0.00
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article

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

Phoebe Arbon, Francisca Samsing, Jasmine Knowles, Jemma L. Geoghegan et al.
Reviews in Aquaculture
Myxozoan Parasites in Aquatic Species
article

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

Phoebe Arbon, Francisca Samsing, Jasmine Knowles, Jemma L. Geoghegan, Oleksandra Rudenko, Andrew C. Barnes, Jane Williams, Jerusha Bennett, Kate S. Hutson, Kerrie Wiley, D Bass, Charles Caraguel, Katherine G. Lockton, Joy A. Becker, Vincenzo A. Costa, Felix Vaux, J Carson, Matthew Arnold, Roisin Sullivan, Garry Knowles, Thomas Dumond, Matthew Pope
article en

Abstract

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.

Reviews in AquacultureVol. 18(4)
The University of Sydney (AU), Centre for Environment, Fisheries and Aquaculture Science (GB), Auckland Institute of Studies (NZ), Royal Veterinary College (GB), University of Auckland (NZ), The University of Queensland (AU), University of Exeter (GB), Services Australia (AU), US Biologic (United States) (US), The University of Adelaide (AU), Cawthron Institute (NZ), University of Glasgow (GB), University of Otago (NZ), James Cook University (AU)
Openalex Percentile: Top 11%
Myxozoan Parasites in Aquatic Species
DOIOpen Access PDFOpenAlex
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