Discussion from a structured expert workshop held at the 2025 Aotearoa Aquatic Diseases Symposium in Dunedin, New Zealand, where experts explored the challenges and opportunities for adopting high‐throughput sequencing (HTS) to support disease investigations in aquaculture is synthesised.
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.
This review synthesises the current state of genomic and transcriptomic resources available for spiny and slipper lobsters (Achelata), contextualising these within the broader decapod framework and proposing future directions integrating genomics, transcriptomics, and functional tools to accelerate sustainable domestication and genetic improvement of lobsters.
Courtney Lewis, Ahmad Farhadi, Susan Glendinning et al.· Reviews in Aquaculture· 0 citations
Since the COVID-19 pandemic, wastewater-based surveillance (WBS) has emerged as a key approach to assess community-level health and the evolution of pathogens. To date, most established WBS systems focus on polymerase chain reaction (PCR) based detection and targeted sequencing of known pathogens because these approaches are well-accepted and include amplification of pathogen target sequences of interest thereby enabling lower limits of detection. Metagenomic next-generation sequencing (mNGS) is a promising approach to enable pathogen detection and surveillance beyond predefined pathogen lists, but its regular application to WBS has not been yet widely adopted because many key performance characteristics are not well-understood, including limit of detection (LOD) and false positive/negative rates. This paper describes a computational analysis to estimate the operational LOD of various sequencing approaches using a simplified model of a local wastewater (WW) system involving a military base. This paper also presents findings from two types of experiments: 1) laboratory-spiked, those for which Atlantibacter subterraneus (Asub) is introduced into real-world WW samples in a laboratory setting, and 2) system-spiked, those for which Asub is introduced at a source location of a real-world WW system. Findings indicate that mNGS detection performance varies with sequencing method and the data analysis process. In addition, findings indicate that site-specific method characterization should be used when implementing mNGS for WBS because sites can have different WW system configurations, background organisms and sequencing inhibitors.
A. Xiao, K. Besse, D. Connors et al.· medRxiv· 0 citations
Fish vaccination has been practiced globally for several decades and is increasingly recognized as a cornerstone of sustainable disease management in aquaculture, offering an effective alternative to antibiotic and chemotherapeutic use. This PRISMA‐ScR guided Scoping Review synthesized evidence from 173 peer‐reviewed studies and reports to evaluate vaccine platform efficacy, administration routes, adoption challenges, and emerging directions. The major findings indicate that across laboratory and field trials, multivalent injectable vaccines in salmonids consistently achieved Relative Percent Survival (RPS) values exceeding 80% against bacterial pathogens such as Aeromonas salmonicida and Vibrio anguillarum, contributing to a documented 99% reduction in antibiotic use in European countries' aquaculture sector. Experimental immersion and oral vaccines for warm‐water species such as tilapia and carp demonstrated more variable efficacy, with RPS typically ranging from 50% to 75%, reflecting challenges in antigen delivery and uptake. Economic analyses from industrial salmon and tilapia farming report positive Benefit–Cost Ratios (BCR) ranging from 2.5:1 to 5:1, driven by reduced mortality and improved feed conversion ratio (FCR). However, for small‐ and medium‐scale fish farms in low‐ and middle‐income countries (LMICs), vaccine adoption remains below 15% due to high upfront costs, cold‐chain limitations, and lack of locally validated formulations. Critical knowledge gaps persist, including insufficient field validation of vaccine efficacy under commercial conditions, the absence of harmonized immune assays to enable cross‐study comparisons, and limited understanding of environmental modifiers such as temperature, oxygen, and stress on vaccine performance. Future research should prioritize integrating epidemiological modeling for disease prioritization and developing affordable, thermostable vaccines tailored to LMIC fish species. Addressing these gaps through targeted investment and partnerships will enhance aquaculture resilience, reduce antibiotic dependency, and strengthen global food security.
Fredrick Juma Syanya, Zachariy Oreko Winam, P. Mwangi et al.· Journal of the World Aquacul...· 0 citations
Wastewater metagenomic sequencing (WW-MGS) enables simultaneous detection of hundreds of pathogens, but its use for quantitative pathogen tracking has not been robustly validated. Like wastewater PCR (WW-PCR), WW-MGS is affected by biases from variable fecal dilution and sample processing, but must additionally contend with the compositional structure of sequencing data, where a taxon's apparent abundance depends on the abundance of every other taxon in the sample. Simple summaries such as a pathogen's fraction of total reads may therefore be poorly suited to quantitative use. We retrospectively evaluated seven normalization approaches that attempt to control for these sources of bias against a baseline of total read relative abundance, using 1,425 samples from the CASPER consortium spanning 25 U.S. sites. Each approach was compared against WW-PCR and clinical data across eight total pathogens. Among the normalization strategies we evaluated, tobamovirus markers, diet-derived plant viruses abundant in human stool, performed best. Normalizing WW-MGS data by tobamovirus-genus counts improved median site concordance for 18 of 19 pathogen and comparison-source combinations. Gains were largest for year-round-circulating SARS-CoV-2 and norovirus and smaller for sharply seasonal pathogens such as influenza and respiratory syncytial virus, where baseline concordance was already high. Tobamovirus normalization rarely degraded concordance, with median gains roughly five times larger than median losses. Tobamovirus-normalized WW-MGS reached clinical concordance comparable to targeted WW-PCR, supporting its use as a quantitative trend-monitoring tool alongside pathogen-agnostic detection.
L. Justen, A. Zulli, R. S. Kantor et al.· medRxiv· 0 citations
This review outlines foundational applications of omics in aquaculture and highlights the characteristics and current applications of distinct omics approaches, and summarizes three core application domains of omics in aquaculture.
Chao Guo, De-Qi Sun, Ben Yang et al.· Fishes· 0 citations
The resistome, defined as the complete set of antibiotic resistance genes (ARGs) present in the microbiota of a given environment, is a critical component for understanding the evolutionary dynamics of antimicrobial resistance (AMR) and its impact on human, animal, and environmental health. This review summarizes current methods and technological advances and offers a forward-looking perspective on resistome research. A systematic literature search was conducted. References on short-read and long-read sequencing, amplicon sequencing, shotgun metagenomics, and multi-omics integration were included, as were bioinformatics tools for the detection, quantification, and annotation of ARGs. The results indicate that next-generation sequencing (NGS) technologies have significantly improved the characterization of ARGs across ecosystems, enabling high-resolution microbial profiling and the discovery of new variants. Furthermore, integrating multi-omics approaches with computational tools improves data accuracy, reduces analysis and reporting times, and facilitates the development of predictive models. However, significant challenges remain, which will be key to strengthening epidemiological surveillance under the One Health approach.
Lenin García Gutiérrez, A. Méndez-Tenorio, M. A. López-Luis et al.· Antibiotics· 0 citations
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