Disease Diagnosis in Aquaculture

Intensification of aquaculture practices and species diversification have resulted in disease outbreaks in farmed aquatic organisms. Disease outbreaks are the major bottleneck to the expansion and development of sustainable aquaculture. In the overall aquatic animal health management strategy to minimize disease risks, early detection of the disease-causing agents is essential. The earlier the disease is diagnosed and treated, the better it is for prognosis and prevention of secondary infections. According to the World Health Organization (WHO), an ideal diagnostic assay for pathogen detection should be rapid, specific, sensitive, instrument-free and cost-effective. The diagnostic procedures can be classified as presumptive and confirmatory based on the extent of precision of the results obtained. Presumptive diagnosis is the preliminary diagnosis of a disease based on clinical signs and symptoms and is made by gross examination and post-mortem findings of the diseased animal. Confirmatory diagnosis involves the definitive identification of the causative agent or its sequelae using techniques such as histopathology, electron microscopy, parasitological, bacteriological, virological, immunological and molecular techniques. FAO/NACA classifies diagnostic levels into three categories, levels I, II and III, based on the technical expertise, facilities and other infrastructures required for disease diagnosis. The sampling procedure, target samples and sample size depend on whether the sampling is for targeted surveillance or routine health monitoring and on the sensitivity and specificity of the diagnostic methods used. This chapter outlines various presumptive and confirmatory diagnostic tests used in aquaculture for assessing and managing aquatic animal health, including numerous modifications of existing methods and their respective advantages and disadvantages. Some of the latest developments in disease diagnosis, such as proteomics, protein–protein interactions, digital droplet PCR, the use of machine learning techniques for disease diagnosis and CRISPR-Cas systems, are also described. Additionally, point-of-care tests that can be used on-farm with minimal equipment are discussed. Finally, various diagnostic protocols reported for the major bacterial, fungal and viral diseases of finfish and shellfish are summarized.