Biosecurity in Aquaculture, Part 1: An Overview

Shane Willis

This factsheet by the Southern Regional Aquaculture Center (SRAC) gives an overview of biosecurity in aquaculture.Biosecurity in aquaculture consists of practices that minimize the risk of introducing an infectious disease and spreading it to the animals at a facility. The risk is that diseased animals or infectious agents will leave a facility and spread to other sites and other susceptible species. These practices also reduce stress to the animals, thus making them less susceptible to disease. 
Over the past decade, several essential disease outbreaks in both U.S. aquaculture (spring viremia of carp, koi herpesvirus) and wild fish populations (viral hemorrhagic septicemia type IVb) have increased the industry’s awareness of the importance of biosecurity. Examining specific points in production when pathogens (disease-causing parasites, bacteria, viruses, and fungi) may be introduced or disease may develop will help producers develop precautionary measures. Good biosecurity minimizes the fishes’ exposure and susceptibility to pathogens, reduces economic losses from mortalities and helps prevent mandatory depopulation.

This publication provides an overview of major concepts in biosecurity for aquaculture. Although it concentrates primarily on finfish, the principles described also hold for other species groups. Because biosecurity management differs with the type of system, two additional publications will cover specifics for the tank and recirculating systems (Part 2) and ponds (Part 3).

Major Goals of Biosecurity

Primary biosecurity goals are:

  • animal management—obtaining healthy stocks and optimizing their health and immunity through good husbandry
  • pathogen management—preventing, reducing, or eliminating pathogens
  • people management—educating and managing staff and visitors

The ease with which a specific pathogen can enter a facility, spread from one system to another, and cause disease depends on:

  • the species, immune status, condition, life stage, and strain susceptibility of the cultured fish;
  • major environmental factors such as water quality, water chemistry, and husbandry practices;
  • characteristics of the pathogen, such as biology and life cycle, potential reservoirs (carriers, other animals), survival on inanimate objects (equipment), options for legal treatment(s), regulatory status (exotic vs. endemic disease, reportability, and federal, state and local laws); and
  • Workers’ understanding of biosecurity protocols and compliance

Animal and Population Management

Obtaining healthy animals (eggs, fry, juveniles, broodstock) from a reputable supplier is critical. Work with a fish health professional to determine species-specific health parameters and diseases of concern. Before obtaining animals from an outside source, learn as much as you can about their health, including where they came from, whether they have had any disease issues, and whether they have had any health examinations, disease testing, or treatments. Some suppliers offer animals that have tested free of specific pathogens, and these animals are preferable. If information about animal health is unavailable or unclear, fish should be tested shortly after they are received. Strains of some aquacultured species are known to be more resistant to specific diseases. Tracking the lineage/ genetics of your broodstock helps avoid inbreeding and ensures the production of healthy gametes and fry. Good husbandry is also vital to biosecurity. Any environmental conditions or procedures that stress the fish or damage the skin, fins, gills, or intestine will weaken their immune systems and make them much more susceptible to disease. Good water quality/chemistry, nutrition, and handling methods will go far toward preventing disease.Good preventive medical practices include quarantine, routine observation, vaccination, and the use of immunostimulants, probiotics, and diagnostics for disease management.

Quarantine is one of the most critical animal management and biosecurity measures. Quarantine is the procedure by which an individual or population is isolated, acclimated, observed, and, if necessary, treated for specific diseases before its release onto the farm or for live market sale (e.g., for grow out or for aquarium fish stores). Quarantine principles apply for new fish coming into a facility, fish moving from one area or system to another within the facility, and resident fish that become diseased. Well-designed quarantine systems physically separate incoming fish from the rest of the farm. Water in quarantine systems also should be separate from that on the main farm, and discharges should be handled appropriately. Proper quarantine protects established populations from potential exposure to pathogens and gives the new animals time to acclimate to water, feed, and management and recover from handling and transport. Handling and transport have been shown to reduce disease resistance, and recovery may take weeks.

Fish in the general population that become sick may have to be isolated in tanks in the same system or room as their healthy counterparts; signs or other methods should alert employees that the population is diseased. Significant quarantine components include all-in-all stocking, isolation or separation, observation, and diet adjustment, and sampling and treatment. All-in-all-out stocking. This involves bringing animals in as a group from only one source population and maintaining them throughout the quarantine period. It prevents exposure to other pathogens not currently in that population. Ideally, no new animals should be added to a group currently in quarantine. All-in-all-out quarantine may involve an entire facility, room, or system.

Isolation or separation.

 A group of animals in quarantine should be physically isolated from other quarantined populations and the resident populations. Methods of isolation should be built into the facility and system design. If logistics prevent complete isolation, populations should at least be separated by tank or vat. Regardless of the level of isolation, appropriate sanitation and disinfection measures must be used to reduce cross-contamination between quarantined and established populations and between separate populations in quarantine.

Observation and diet adjustment. 

 Animals should be observed for normal and abnormal appearance and behaviors throughout the quarantine period to detect disease problems early. Loss of appetite, for example, is a prevalent early sign of disease. Good nutrition will increase disease resistance, and careful adjustment from the diet of origin to the on-farm diet will reduce problems from sudden changes. 

Sampling and treatment.

Fish in quarantine should be sampled for specific diseases of concern at the beginning and end of the quarantine period and when disease signs develop. Although complete necropsy evaluation of many specimens is best, limited sampling of more valuable specimens can be done without sacrificing the animals by examining small sections of skin, fin, and gills for parasites and doing a blood culture for systemic bacterial infections. The results can then be used to improve quarantine methods and the use of drugs. Consult with a fish health professional to assist with this. Legal issues associated with drug usage should be considered before treatment.

Pathogen Management

Not all pathogens (disease-causing organisms such as bacteria, parasites, viruses, and fungi) are equally concerned. Pathogens vary in their regulatory significance, survivability in reservoirs, pathogenicity (how easily they can infect and cause disease), diagnostics, and control. Although some pathogens cause disease more readily than others, environmental and host factors—especially the species and its immune status—will ultimately determine whether fish become sick.

Regulatory significance.

Some diseases and pathogens are considered necessary internationally and listed by the OIE (World Organization for Animal Health) because of their economic or environmental importance. Many of these, or others, are also currently regulated or under regulatory consideration by the USDA?APHIS and by state and local governments. Outbreaks of some of these diseases require depopulation, which will significantly affect the operation. The proper authorities (local, state, and federal) must be notified if a reportable disease is suspected or diagnosed in your facility. Work with a fish health professional to determine if your species is susceptible to any regulated diseases, and get professional assistance with disease diagnostics and management.


Pathogens can survive and thrive in "reservoirs" within a facility. Non-living reservoirs include water, system components, equipment, floors and walls, and feed. Living reservoirs include the aquacultured animals themselves, other animals (such as frogs and birds), plants, and live (or frozen) food. Understanding the biology of pathogens is essential, including the factors that permit them to survive in reservoirs and how easily common disinfectants can kill them.

High animal densities, biofilms, and sediments can help concentrate microorganisms. Uneaten feeds and other organic matter in the system favor pathogen survival and spread. Aeromonas and Vibrio species are bacteria that prefer these highly organic environments. They can also infect and live within a fish, sometimes without causing disease. Another group of bacteria, the Streptococcus species, are not as common as Aeromonas and Vibrio but are challenging to eliminate once established within a system. Mycobacteria also live within biofilms that coat the tanks, filters, and pipes. Some parasites, including trichodinids, sessile ciliates, Tetrahymena, and Uronema, thrive in organic wastes and dead or dying fish. Viruses vary in their ability to survive, but some viruses may persist for weeks or months. Likewise, fungal spores can survive for a long time in detritus.

Pathogens can enter facilities in aerosols (fine water droplets), on equipment and vehicles, and people's hands, arms, and feet. Once inside, they may survive in pockets of moisture on the ground, walls, or ceiling.

Pathogens can also be spread by other animals that live in or near ponds or tanks (birds, rodents, reptiles, insects, aquatic invertebrates). For example, midge fly egg masses (which develop into larvae sold as bloodworms) have been shown to harbor some Vibrio species. In addition to directly transmitting some pathogens, animals may also serve to complete parasite life cycles (e.g., white or yellow grub—digeneans, and myxozoans such as those that cause hamburger gill disease in catfish).

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