Submission of fish for disease diagnosis

Fish diseases

Mass mortality of farmed silver perch (Bidyanus bidyanus) Photo: Stuart Rowland


For aquaculture stock, optimum farm design, appropriate husbandry, water quality management, and regular health monitoring all help to minimise disease outbreaks on farms. However at times, the farmer will experience disease problems, often resulting in stock losses. When the disease cannot be diagnosed on-farm, samples of the infected fish should be submitted to a diagnostic laboratory, and it is a condition of every land-based aquaculture permit that:

The permit-holder shall notify the department within 24 hours of the discovery of any declared disease …, unusual disease or any significant event associated with the welfare of the fish on the premises  (e.g. unexplained or significant fish mortalities, >5% of fish stock loss in a week).

In the event of a declared disease, unusual or otherwise significant mortality, within 24 hours, contact:

Samples should be prepared for submission to a diagnostic laboratory as described below, or as directed by DPI in accordance with guidance received at the time of reporting the event.
The importance of packaging appropriate samples for diagnostic purposes cannot be over emphasised. The selection and packaging of the samples together with the accompanying information often determines the success or failure of the diagnosis.

On-farm diagnosis

Disease diagnosis begins on the farm. With the use of suitable equipment including water quality meters, a microscope and a dissecting kit a number of diseases, such as some external parasitic diseases, can be diagnosed on site. As a result, farmers can quickly act to reduce impacts of diseases and parasites.

Specimen selection

Many pathogens (disease producing organisms) die or leave soon after the death of the fish, or their presence is masked by decomposition. Consequently, fish found dead in the water are of no or little value for diagnostic purposes. If the disease is sufficiently severe to cause deaths, the remaining living fish may be infected with some of the pathogens. Ideally a range of clinically affected individuals should be sampled including those in early stages of disease, those displaying unusual behaviour and moribund (nearly dead) individuals. If fish of all sizes are affected, small specimens are easier to transport.

Live fish are the most desirable for reliable diagnosis, however transporting live specimens to the laboratory can be very difficult. If submission of live specimens is not possible, then freshly euthanased specimens should be kept on ice and sent unfrozen, provided they arrive at the laboratory as soon as possible (ideally within 24 hours). A final option is to send specimens preserved in formalin or other fixative (contact NSW DPI for further advice). In all cases, the sample should include affected specimens.

Shipment of specimens

Live specimens- Using one or two strong plastic bags, fill 1/3 full of water (preferably using the water the fish came from). Place the sampled fish (approximately 4 to 6 fish) in the water, squeeze out the air, then fill the bag with compressed oxygen making sure the air does not escape during the removal of the air delivery line. Twist and double over the neck of the bags and securely tie using tape, cord, or rubber bands. The bags should then be packed in a watertight container, sealed and clearly labelled "Scientific Specimens - Perishable" followed by the delivery address. During hot weather the specimens may be kept cooler by using crushed ice next to the container housing the fish. Overnight transport is essential. Do not feed fish prior to transport.

Iced specimens- After collecting the fish, wrap in a damp cloth or paper towel. Place the sample in a plastic bag and cover with ice or ice packs/bricks. Shipment should be in a well-insulated container with a generous quantity of ice or ice packs/bricks. Place in a watertight container and clearly label. Do not ship iced fish if delays are expected (such as over the weekend), as decomposition will render the sample unsuitable for diagnosis. Specimens should be received for examination within 24 hours.

Preserved specimens- Place the specimens in a plastic bottle using a ratio of at least 10 times the volume of fixative to that of tissue. If the fish is more than 5mm thick or greater than 5cm in length, an incision should be made anterior to the anus, and the operculum should be carefully removed to allow the penetration of the preservative into the body cavity and the gills. In the case of larger specimens, the organs or lesions under investigation should be dissected out and transferred into fixative. Skin lesions sampled this way should also include an adjacent region of normal tissue. Fill the container with 10% formalin. Seal the container, place it within another watertight container and label correctly.
Preserved specimens are required to be packaged in three watertight containers and labelled clearly prior to submission under International Air Transport Association (IATA) transport regulations. Check with your courier to ensure packaging meets recommended standards.

Internal organs

Figure 1. General location of internal fish organs

Frozen specimens- Frozen samples should only be considered as a last resort for disease diagnosis as some viruses, bacteria and parasites are inactivated or lost during freezing making identification impossible. However freezing of specimens is recommended for toxicological analysis providing the samples are frozen as soon as possible following the suspected poisoning.

Information to accompany specimen

It is important to provide as much information as possible with the specimens. Where possible this should include:

  • Name; address; phone number; email address and date
  • Species of fish; age; average size; disease suspected
  • Water quality including pH; temperature; dissolved oxygen; ammonia; salinity
  • Type of system or production facility e.g. pond; tank; raceway
  • Stocking density
  • Date mortality began and mortality rate
  • Clinical signs e.g. poor feeding; abnormal swimming; "flashing"; sudden death
  • Water source
  • Diet; size and manufacturer; ration; storage
  • Recent husbandry/handling e.g. harvesting; grading; water exchange; new fish introduction
  • System changes e.g. new tanks; changes in diet; chemical treatments
  • General observations; environmental changes; weather conditions.

This information needs to be submitted along with the completed;

Further information relating to sample preparation and submission may also be found in the State Veterinary Diagnostic Laboratory webpage, or by contacting:

State Veterinary Diagnostic Laboratory
Elizabeth Macarthur Agricultural institute (EMAI)
Phone: 02 4640 6333
Fax: 02 4640 6300

What steps can be taken to control losses while waiting for results?

Individual laboratories vary in the amount of time required to process samples and communicate the results to the submitter.
Microbiology (bacterial isolation, identification and sensitivity; virology; identification of virus), and histopathology (microscopic examination of specially prepared tissues) may take between 2 to 14 days for completion. Results of post mortem examination should be available sooner.

While waiting on results, the best approach is to:

  • Remove mortalities from the pond and improve water quality through cessation of feeding, additional aeration and water exchange.
  • Isolate affected ponds or tanks and equipment and quarantine from other ponds or tanks. minimise stock movements both within the facility, and stocking to other water bodies, in case you may be spreading an infectious agent (e.g. virus, new parasite).
  • Dispose of effluent water in a biosecure manner, such as after appropriate disinfection and ensuring it does not enter waterways. Do not recycle effluent water.
  • For market size fish, food safety issues should be considered. For further information on food safety issues contact the NSW Food Authority (