Idaho Fish Health Center
Pacific Region



The Idaho Fish Health Center  offers a full service bacteriology department  from diagnostic to confirmation.  Following the AFS  Blue Book flow charts, we use individual biochemicals,  Biolog and Bio Merieux API system  biochemical assays for the identification of bacteria.


ELISA  stands for the Enzyme-Linked Immunosorbent Assay.  It is an assay or test, used to detect the level of the bacteria, Renibacterium salmoninarum, which is the causative agent for Bacterial Kidney Disease (BKD).  BKD can cause  many problems and high mortality rates in salmonids, especially spring chinook salmon. It can occur as an acute outbreak with many losses, or it can be chronic with low levels of mortality rising with stresses and other pressures on fish.  It can be horizontally transmitted, from fish to fish via the water, or it can be vertically transmitted, from female to her eggs.  Once a fish has BKD, it is very difficult for the fish to overcome or  be cured of since the R. salmoninarum bacteria can reside , still alive, inside of the fish's immune cells.  The antibiotic erythromycin is often used in medicated feed under an INAD and can decrease mortalities, but will not rid the fish of the bacteria.  Many hatcheries will also inject female adult chinook salmon with erythromycin before spawning to help decrease the likelihood of vertical transmission to the egg.

At the IFHC, as well as many other fish health centers and labs, the ELISA is used to help manage BKD in fish. At the Dworshak National Fish Hatchery, which is co-located with IFHC, fish health biologists take random kidney samples from steelhead adults (male and female) and  male chinook.  Because spring chinook salmon are more susceptible to the disease, and are more likely to vertically transfer the disease, 100% of the spring chinook females are sampled as they are spawned at the hatchery.  In this way, the level of R. salmoninarum found in each female can be assessed and categorized as to high, medium, or low risk of the bacteria levels in the corresponding eggs of each female.  Eggs can then be grouped according to their level of the bacteria in order to decrease the risk of horizontal transmission and infections as the fish grow.

ELISA is also used by the IFHC to monitor the levels of R. salmoninarum in fish as they are raised at federal hatcheries in Idaho.  In addition, samples are taken at pre-release exams to assess the levels of the bacteria before the fish are released from the hatchery to migrate to the ocean.

PCR (Polymerase Chain Reaction)

Polymerase chain reaction (PCR) is a technique which is used to amplify the number of copies of a specific region of DNA, in order to produce enough DNA to be detected.   This technique can be used to identify with a very high-probability, disease causing viruses and/or bacteria, a deceased person, or  a criminal suspect.  ( Remember the O. J. Simpson trial??)

To be able to use PCR to identify a bacteria or virus, we need to know  the exact gene sequence  of a particular region in the DNA  for a particular  bacteria or virus.  Each kind  or species of virus or bacteria has a different sequence  for that particular area of DNA; species of the same bacteria  or viruses  of the same kind have their own unique sequences  and can be identified by these  sequences.

At the IFHC we use primary isolation techniques to find bacteria, virus  and parasites and use PCR for confirmatory purposes.   "Primers" (synthesized single strands of DNA which have the exact flanking sequences to known pathogens) have been developed for C. shasta,  M. cerebralis, F. psychrophilum, R. salmoninarum, IHNV, VHS, and several others.

Virology/Cell Culture

Virology is the study of viruses. Viruses are obligate parasites of living cells that are unable to reproduce on their own and therefore depend on the living cells for reproduction. Most viruses are host and tissue specific. Many viral infections are asymptomatic, no visible signs, but can be symptomatic, with visible or clinical signs, causing such symptoms as inflammation and hemorrhaging.

Kidney and spleen samples are tissues of choice for viral testing. Ovarian fluid, gills, brain and skin samples are a few other tissue types that can also be infected with virus. Virus come in many different sizes, shapes and characteristics. Some cause tumors (Oncorhynchus masou virus - OMV), while others actually kill host cells when viral replication is complete (Infectious hematopoietic virus - IHNV). It is this cytopathic (cell damage) effect (CPE) that is seen in laboratory cell cultures.

Because the virus is so small detection can be difficult. Detection usually starts with the sample showing CPE on a desired cell line. The cell lines are maintained in-vitro, growing in a plastic flask, and different cell lines must be maintained to detect virus in different species.  Most virus are tissue and host specific. Once the sample has been prepared and added to the correct cell line it must be monitored frequently to watch for changes (CPE) in the cells.

The Idaho Fish Health Center routinely tests for viruses in returning adult Steelhead trout and Spring Chinook salmon at Dworshak and Kooskia National Fish Hatcheries. Virus normally found in these returning adults is IHN. IHN is spread from fish to fish through the water. Diseased fish can become lethargic (sluggish) and dark in coloration. Gills can often be pale due to anemia which can be caused by hemorrhaging of tissues in the fish such as the vent and the base of the fins. The body cavity may also contain fluid.

In addition, Idaho Fish Health Center tests for certifiable viruses at 6-9 private hatcheries in the states of Idaho and Wyoming, and tests for viruses in wild fish populations in conjunction with the National Wild Fish Health Survey.


Histology involves the technique of preparing tissue for microscopic examination. Tissues must be processed through a series of steps including fixing, dehydrating, clearing, embedding, cutting, and staining.  Once the tissues are prepared, sliced very thinly, stained, and placed on a slide, they can be examined through a microscope.

At the Idaho Fish Health Center, histology is used to look at fish tissues and organs to help determine a diagnosis, to examine a disease process, or to confirm pathogen identification, such as Myxobolus cerebralis (the causative agent of Salmonid Whirling Disease.)  It has also been used with nutritional growth studies on fish.

Federal Hatchery Monitoring

The fish health biologists of the Idaho Fish Health Center (IFHC)  provide diagnostic, monitoring, and inspection services for three Federal fish hatcheries in Idaho; Dworshak National Fish Hatchery, Kooskia National Fish Hatchery, and Hagerman National Fish Hatchery.

When mortalities increase at one of IFHC Federal  hatcheries, the IFHC staff collect live and moribund fish  to determine the cause of death .  They look for viral, bacterial and parasitic pathogens.  Once a diagnosis is determined, a treatment is recommended.

Periodic monitoring of some fish species, such as chinook salmon  for Bacterial Kidney Disease (BKD),  must be done to assess the health of fish prior to release into the wild. 

Prior to fish being release into the wild from any Federal fish hatchery, a pre- release inspection must be done to determine the health of the fish.   If any certifiable pathogens are found, they must be treated  to help prevent the spread of fish diseases.

Commercial Inspections 

In order to sell or transport fish or eggs across state and international borders, private fish growers need a certificate stating their fish are free of fish pathogens.  Every "lot" of fish, which are separated by  age class or those on separate water systems, must be examined to statistical significance (usually 60 fish per lot).  The Idaho Fish Health Center (IFHC) provides inspections for private and commercial growers in Idaho.  This includes viral, bacterial, and in some cases, parasitic pathogens, depending on importation regulations of the state or country receiving the fish.  Once all assays are complete, a certificate is given to the grower and to the buyer of those lots of fish. 

The IFHC currently performs  regular inspections for 5 private hatcheries.  Because some commercial growers sell to Chile and Japan, they require certification from a USDA APHIS certified Lab.   IFHC is a USDA APHIS certified lab.

National Wild Fish Health Survey

The IFHC  is one of 4 FHC's in Region 1  that participates in the National Wild Fish Health Survey (WFS).  Since the WFS  began, the IFHC  has collected and assayed over 5900 fish from approximately 400 sites. We continually look for new partners in our efforts.

                lab sampling    electrofishing       

All photos USFWS

For more information on the National Wild Fish Health Survey or the federal fish health center nearest you, please contact Laura Sprague at (208) 476-9500  or see the WFS web page  located at  

Investigational New Animal Drug (INAD)

INADs are drugs that have not been approved by the Federal Drug Administration (FDA) for certain uses or at certain doses, but are under investigation or testing.  In fish culture, there are extremely few drugs available that have been approved by FDA for treating pathogens and diseases of fish.  Fish pathogens include parasites, bacteria, and viruses.  To help alleviate this situation, the FDA has allowed for the use of a few specific drugs on fish which have not yet been approved, through the INAD process.  The INAD process permits testing and trials to be conducted using these drugs at fish hatcheries and commercial ponds.  The results from these studies are used to contribute to the data needed by FDA in order to approve these drugs for use on fish, or to extend their label use on more diseases in fish, or at different water temperatures, or doses.

The IFHC monitors the use of drugs under INADs at the federal hatcheries in Idaho.  Paperwork including specific forms must be filled out each time a drug is used under an INAD.  These forms include information concerning the receipt of the drug, inventory, use, mortality rates, and disposal.  The IFHC ensures that the forms are filled out properly and completely before sending them on to the National INAD Officen Bozeman, Montana.  There the forms from fish facilities across the country are collected and compiled into a package to be sent to the FDA for drug approval.

If you have questions or comments, please contact us or call us at (208) 476-9500.

Last updated: June 1, 2015
Idaho Fish Health Center
Pacific Region Fisheries Resources Home
Pacific Region Home

U.S. Fish and Wildlife Service Home Page | Department of the Interior  |  | About the U.S. Fish and Wildlife Service  | Accessibility  | Privacy  | Notices  | Disclaimer  | FOIA