Infectious diseases represent one of the major challenges and limitation to sustainable aquaculture. They can have major impacts on animal welfare, livelihood of farmers and threaten the health of captive stocks and wild populations. Pathogens can spread through movement of live fish, fish products, water and shared equipment. Routine screenings of pathogens in aquatic animal production systems are important to minimize the risk of their introduction, transmission and spread. On suspicion of a disease during abnormal mortalities, investigation with collection of biological samples from moribund animals must take place rapidly for disease diagnostics. Quality biological sampling is a fundamental requirement for all kinds of disease diagnostic and pathogen screening work. WorldFish and partners developed this rapid guide on sampling materials required for fish disease diagnostics. It lists all the personal protective equipment, the data collection/recording/cleaning supplies and sampling materials: consumables, reagents, media and tools needed to conduct one of the six quick fish sampling guides for disease diagnostics: 1. Wet-mount sampling guide (for ectoparasites & fungi) 2. Fish & water Microbiome sampling guide 3. Blood sampling guide 4. Bacteriology sampling guide 5. Molecular and virology sampling guide 6. Histology sampling guide.

A free online course on foundations in fish disease sampling is also available via Learn.ink.

Parasitic and fungal infestations represent one of the major challenges to sustainable aquaculture. As part of routine health checks or during abnormal mortality events, screening for ectoparasites and fungi in tilapia, carp and catfish production systems is important to minimize the risk of their introduction, transmission and spread. WorldFish and partners developed this quick guide for ectoparasites and fungi assessment under a light compound microscope. Standard wet-mount specimens consist of gill biopsy (gill clip), fin biopsy (fin clip) and skin scraping (mucus smears). Additional smears may be included in the presence of external lesions/ulcers (eye, skin, mouth). A free online training course on wet mount sampling is also available via Learn.ink.

Interactions between microbes associated with the host, other organisms present in the system and the environment itself are increasingly recognised to contribute to aquatic animal diseases. Those microbiome assemblages and their functions are extremely diverse and poorly understood. They vary over time in water and between host tissues and organs.

High-throughput sequencing technologies (multi-omics) and bioinformatics analysis of complex microbiomes can provide biological insights offering new opportunities for early detection of pathogens and disease mitigation strategies. Similarly, such approaches are being applied to study the effect of locally available ingredients for use in fish feeds and their impact on fist gut microbiome and the health of the pond environment—optimising the growing conditions on-farm.

WorldFish and partners developed this quick guide for microbiome sampling from fish skin/gills mucus swabs, internal organs (e.g. gut) and water samples from ponds, hatcheries tanks, river, and canals.

A free online training course on microbiome sampling is also available on Learn.ink.

Fish blood sampling requires specific techniques and skills that are fundamental for all kinds of analyses such as haematology, chemistry analysis, parasitology/bacteriology investigation, antibody titration, molecular diagnostic and many others. WorldFish and partners developed this quick guide on blood sampling from fish for: (1) blood serum isolation, (2) blood plasma isolation, (3) blood DNA extraction, (4) blood RNA extraction, or for (4) blood smear preparation on microscope slide. A free online course on blood sampling is also available via Learn.ink.

Bacterial diseases represent one of the major impediments to sustainable aquaculture. Routine screening for bacterial pathogens at various life stages of tilapia, carp and catfish a are important to minimise their introduction into production systems and before they can cause serious diseases and spread to new areas. During an abnormal mortality event, routine sampling for bacteriology from moribund animals should take place rapidly as part of the disease diagnostic investigation. Bacteriology is the culture and identification of bacteria growing under specific conditions. WorldFish and partners developed this quick guide on fish bacteriology sampling. Standard bacteriology is a swab taken from the caudal or anterior kidney and inoculated onto agar (e.g. Tryptone soya agar) to screen for systemic bacterial infection. Additional swabs may be included in the presence of external or internal lesions/ulcers (e.g., eye, skin, mouth, liver, spleen, brain). A free online training course on bacteriology sampling is also available via Learn.ink.

Major pathogens of fish and other farmed aquatic animals include bacteria, fungi, viruses and parasites. These can lead to serious infectious diseases and losses representing one of the major limitation to sustainable aquaculture. Routine health checks for key priority pathogens of tilapia, carp and catfish—will vary with geographies—are important to minimize the risk of their introduction, transmission and spread. On suspicion of an unknown disease during abnormal mortalities, it is routine for the investigators to collect clinical samples from moribund fish for molecular and virology diagnostics. Molecular diagnostics are techniques used to amplify small DNA/RNA sequence(s) that are unique to a particular pathogen to ascertain their presence or absence. Virology is a branch of microbiology that study viruses and viral diseases. WorldFish and partners developed this quick fish sampling guide for molecular and virology diagnostics. Standard specimens for general molecular and virology health evaluation include kidney, liver, spleen, brain and gills. Other tissues may be collected.

During investigation of an abnormal mortality event, fish tissues (or biopsies) for histopathology analysis are collected for disease diagnosis. Histology consists in the preparation of thin, stained tissue sections for microscopic examination to study their structure and function. Histopathology is the study of disease and disease processes by looking at the change in the anatomy or anomalies from cells, tissues and organs as seen through a microscope. WorldFish and partners developed this quick fish-sampling guide for histology. Standard biopsy specimens for histological examination consists of fixed sections of brain, gill, heart, intestine, kidney, liver and spleen. Other tissues may be collected in the presence of external lesions/ulcers (e.g., eye, skin, muscle). A free online training course on histology sampling is also available via Learn.ink.