Fish Health Center
Fisheries Resources
Pacific Region

Fish Health Program: Understanding Disease Diagnosis

Causes of Disease

Fish health can be affected by environmental problems, nutritional problems, water quality, infectious diseases, and both man-made and natural toxins. Infectious diseases can be caused by viruses, bacteria, parasites, and fungi.

Viral Hemmorhagic Septima Renibacterium Salmoninarum Ichthyophthirius multifiliis (ich) SaprolegniaS
Cultured fish cells being killed by the Viral Hemorrhagic Septicemia (VHS) virus. A common virus in wild Pacific salmon and herring. (Credit: J. Winton, B. Batts) A stained kidney print from a fish infected by Renibacterium salmoninarum, the bacterium that can cause bacterial kidney Disease (BKD) in salmon and trout. The purple spots are the BKD bacteria. (Credit:David Thompson/USFWS)
Ichthyophthirius multifiliis (ich) a common single-celled parasite of wild fish that finds its way into hatcheries through their water supplies (often streams and rivers that harbor wild fish populations). (Credit: Andy Goodwin/USFWS) Saprolegnia, a water-mold that grows on fish when their immune systems are not fully functional.  It is commonly found on adult salmon that have diverted their energy reserves to migration and spawning. (Credit: Andy Goodwin/USFWS)

Diagnosing & Detecting Diseases

Gyrodactylus Trichodina Epistylus Small parasites are diagnosed by looking at gills and mucus under a microscope. (At left: Gyrodactylus, Trichodina, and Epistylus parasites)

F. columnare in culture (Credit: Andy Goodwin/USFWS) A. salmonicida in culture

Bacteria are often found by cultures of fish tissues on jelly-like nutrient agar (At left: Columnaris and A. salmonicida cultures)

CHSE-214 cell line infected with the Infectious Haematopoietic Necrosis virus

CHSE cell line infected with Viral Haemorrhagic Septicaemia

EPC cell line infected with the VHS virus

Viruses are often detected by putting fish samples in plastic flasks that contain a layer of living fish cells. Dying cells mean that a virus may be present.

Hover over the images to the left to see the difference between healthy cells in the first image, and dying cells in the second image.

ELISA plate

Bacteria can also be detected by using antibodies attached to fluorescent dyes or other labels. We use an Enzyme-linked immunosorbent assay (“ELISA”) to detect Bacterial Kidney Disease (BKD) bacteria in the organs of salmon and trout.

(At left: ELISA plate/USFWS)


The labs also use modern techniques like a polymerase chain reaction (PCR), the DNA-based method used in police work and made famous by shows like “CSI.”  The PCR method can be used to detect just a few viruses or bacteria in a sample of fish tissue.  The PCR method makes billions of copies of the virus or bacterial DNA molecules and these copies are detected with fluorescent dyes.

(At left: A PCR gel sample/USFWS)

MC spores under a microscope

Our least favorite test is for whirling disease.  Whirling disease is caused by a microscopic parasite that grows in the skulls and cartilage of young fish. To find it we must digest fish heads in enzymes, grind up the bones and cartilage, then concentrate the parasite spores and search for them under a microscope (shown at left). The PCR method may replace this old “grind and find” approach, but not until everybody is convinced that the new PCR tests are as sensitive as the old method.

(At left: MC spores under a microscope/USFWS)

Methods for the detection of fish diseases are set by national and international agencies and organizations that include the USDA, the World Organization for Animal Health (OIE), and the American Fisheries Society Blue Book (a joint venture by the society, the FWS, NOAA, and APHIS)!

About Our Program

The veterinarians and biologists of the Pacific Region Fish Heath Program protect the health of salmon on Service and many tribal fish hatcheries, and also work to detect and mitigate disease problems in fish populations living in the wild. Historically the Pacific Region operated three Regional Fish Health Centers, but in 2017 the laboratory functions of these Centers were consolidated and collectively renamed the “Pacific Region Fish Health Program.” The program is managed by Dr. Andrew E. Goodwin.

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Fish Health Photos

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Examine a Fish!

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Pacific Region Field Notes

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