Background

The U.S. aquaculture industry is dependent, among other factors, on the control of endemic, emerging and catastrophic diseases that result in losses of aquatic animal production.  Despite the progress that has been made in aquatic animal health, significant losses to disease still occur.  Estimated losses to all aquatic animal producers are about $1 billion annually in the U.S. alone.  The lack of adequate technologies for early and rapid detection, prevention and treatment of diseases has hindered the growth and competitiveness of the U.S. aquaculture industry.  Some tools have been generated to detect the major disease agents in aquatic animal production, but few can be used on the farm.  Testing of these tools at production systems to show the U.S. farmers the practical value of being able to detect the disease agents in a rapid fashion is needed.  Effective vaccines against ESC have been developed by ARS and are being used in health management plans by aquatic animal farmers.  Further research is needed to provide new vaccines and methods for mass vaccination of aquatic animals as is utilized in other food animal industries.  Only a few drugs are approved for treating sick fish.  The overall strategy is to develop health management technologies and biosecurity plans that are safe for the environment and for the consumer of aquaculture products.

Vision

Establish a globally competitive, sustainable aquaculture industry in the U.S. through the development of successful aquatic animal health management strategies that will limit losses to disease, permit lower production costs, and improve product quality.

Mission Statement

Conduct high quality, relevant, basic and applied research and technology transfer to solve problems related to aquatic animal health.

Impact

The development of new animal vaccines and medicines as well as the establishment of health management strategies that can be used  by aquaculture producers will decrease the impact of infectious and non-infectious diseases in U.S. and world aquaculture.  Annual savings of about $700 million by a 70 % reduction in disease losses may be realized.

Linkages

Other USDA-ARS National Programs: 101 Food Animal Production, 103 Animal Health, 105 Animal Well-Being and Stress Control, 108 Food Safety.

Other Agencies and Departments:  U.S. Colleges of Agriculture and State Agricultural Experiment Stations, U.S. Colleges and Schools of Veterinary Medicine, U.S. Fish and Wildlife Service, U.S. Environmental Protection Agency, USDA-APHIS-CVB, USDA-APHIS-VS, U. S. Food and Drug Administration.

Private sector:  U.S. Aquaculture and Grower Associations, U.S. Aquatic Animal Farmers, U.S. Vaccine, Diagnostics and Medicine Manufactures.

Problems to be addressed

a.  Pathogen identification and disease diagnosis

Methods and reagents to rapidly (within hours) detect pathogens and diagnose diseases in aquatic species are still unavailable or have not been applied at the farm.  Methods and reagents to identify strains of aquatic animal pathogens also need to be developed.  Automated detection systems are currently not available or in use.  Further, non-lethal tests are needed in detection and diagnostic methods.  Accurate determination of preclinical infections (i.e., prior to disease) will enhance the opportunities to determine the potential risk of disease occurring and allow for earlier intervention with preventative measures to reduce or eliminate the impact of emerging or catastrophic diseases in the U.S.  Domestic and international trade of aquatic animals needs rapid, automated and accurate tests to demonstrate that aquatic animals, seed stocks and products are free of harmful pathogens to prevent the introduction and spread of harmful diseases.

Goals

1.      Develop rapid and automated methods to detect infectious and non-infectious pathogens and toxins in aquatic animals.

2.      Apply the rapid and automated detection methods to protect U.S. trade, food and aquaculture industries.

3.      Develop methods that allow the identification of strains and sources of the pathogen prior to overt disease.

4.      Develop non-lethal detection and diagnostic methods for aquatic animals.

Approaches

1.      Rapid species-specific polymerase chain reaction (PCR) tests will be developed using nucleic acid (DNA or RNA) sequence information from important aquatic animal pathogens.

2.      Monoclonal and polyclonal antibodies will be produced against specific antigens that will be used in immunoassays to identify serotypes (strains) of major aquatic animal pathogens

3.      Monoclonal and polyclonal antibodies will be developed against the heavy chain of immunoglobulins of fish and used in immunoassays to monitor humoral responses to pathogens and vaccines.

4.      BIOLOG, whole cell fatty acid methyl esters (FAME), amplified fragmented length polymorphic and enterobacterial repetitive intergenetic concensus (ERIC) sequence methods will be used to help “fingerprint” strains of pathogens.

Outcomes

• Rapid, early and automated detection of pathogens, diseases and carrier states will be realized using immunoassays and PCR in non-lethal formats. 
• Rapid, early and automated detection methods will be applied on farms and by USDA- APHIS and State Animal Health facilities. 
• Techniques for identification and serotyping pathogens prior to disease will be realized.

ARS Locations

• Auburn, AL 
• Stoneville, MS 
• Stuttgart, AR 
• Orono/Franklin, ME

b.  Vaccines and medicines

Aquatic animal farmers have a lack of available vaccines and medicines to either prevent or treat infectious and non-infectious disease agents.  Development of new vaccines will likely rely on similar techniques that are currently employed such as killed, modified live, DNA and recombinant technologies.  However, new and novel approaches for development of vaccines may be employed with information obtained from microbial genomics.  Vaccination strategies for mass vaccination will also need to be addressed.  Presently, some vaccines are available but are only effective when administered by injection or with adjuvant.  These treatments are impractical and not usually economically feasible.  The ultimate goal of vaccine research is to develop a product that is safe, easy to administer and effective on the farm.  The approach to new aquatic animal medicines will require novel strategies for identification of effective medicines that are safe to the environment, to the target animal, and to the consumer.  A better understanding of the pharmacokinetics (i.e., dose, uptake, residue accumulation, reactions, safety) of currently available and new medicines is needed.  Methods for delivery of new or approved medicines also need to be studied.  Strategies such as oral application, improving palatability and/or the use of water treatment must be determined.  Cooperation in the approval process and application of medicines is needed for establishment of safe medicines legal for use in aquatic animals.

Goals

1.      Develop safe and effective vaccines and medicines for prevention and control of economically important pathogens of aquatic animals.

2.      Identify effective mass delivery strategies for aquatic animal vaccines and medicines.

3.      Conduct research and development to support approval and licensing of new aquatic animal vaccines and medicines.

Approaches

1.      Produce vaccines and medicines that can be experimentally tested in the laboratory for safety and effectiveness.

2.      Apply vaccines and medicines using mass delivery strategies in on farm trials.

3.      Design studies to evaluate the phamacokinetics of new aquatic animal medicines.

4.      Evaluate the safety and effectiveness of new aquatic animal vaccines and medicines in approved trials to aid the licensing agencies (i.e., USDA-APHIS-CVB, FDA).

Outcomes

• New killed, modified live, DNA and recombinant vaccines and methods for mass vaccination will be developed. 
• Environmentally friendly, effective and food safe medicines to treat aquatic animal diseases will become available.

ARS Locations

• Auburn, AL 
• Stuttgart, AR 
• Leetown, WV 

c.  Immunology and disease resistance

Limited information is available on immune system function of economically important species of aquatic animals.  The lack of information is partly due to the lack of methods and reagents available to study the immune response of fish.  Historically, most research has been invested in human and other production animal immunology.  Part of the reason for the lack of information is that reagents developed in other animal species to identify immune cells and humoral components do not always react with fish cells and components.  New reagents need to be developed that correctly identify the immune cells and humoral components of the fish immune system.  Little information is available on the immune response of the cells in the fish skin, gut, mucus tissue, and nare.  This information is important to understand the first line of defense in fish due to the intimate contact with the surrounding water.  More information is needed on factors such as genetics, the environment, husbandry, stress, nutrition, species of fish and the pathogen that influence disease resistance and immunity in fish.  Future studies will likely concentrate on the immune response of the fish following vaccination. 

Goals

1.      Develop methods to characterize cells and regulatory substances (cytokines) important in natural resistance and acquired immunity in aquatic animals.

2.      Assess the importance of the immune response (i.e., antibody or cell mediated) following vaccination that results in the protective immune response.

3.      Answer basic questions about the immune responses of the skin, gut and nare to economically important pathogens.

4.      Answer questions about the influence of various factors (i.e., environment, genetics, nutrition, husbandry) that affect innate and acquired immunity. 

Approaches

1.      Use fundamental knowledge obtained from animal immunology to design studies to isolate and characterize cells and cytokines of aquatic animal immune systems.

2.      Characterize the natural and acquired immune responses by isolation and characterization of important immune cells and/or immune molecules from the fish skin, gut and nare.

3.      Identify the mechanisms of protective immune responses following vaccination.

4.      Identify the importance and interactions of genetics (i.e., individual variation), the environment (i.e., temperature, season, photoperiod), stress (i.e., water quality, pollution, stocking density, handling and transport, etc.), nutrition (feed quality and quantity, micronutrients, etc.), aquatic animal (i.e., age, species or strains) and pathogen (exposure level, type, serovar, virulence) on innate and acquired immunity. 

Outcomes

• The cells and cytokines important in natural resistance and acquired immunity in aquatic animals will be characterized. 
• The immune response following vaccination that results in protective immunity against the economically important pathogens will be determined. 
• The immune responses of the skin, gut and nare will be characterized. 
• The importance and interactions of environment, stress, genetics, nutrition, husbandry, aquatic animal and pathogen that affect innate and acquired immunity will be determined. 

ARS Locations

• Auburn, AL 
• Stuttgart, AR 
• Stoneville, MS 
• Leetown, WV 
• Orono/Franklin, ME

d.  Mechanism of disease

The understanding of the pathogenesis of aquatic animal pathogens at the cellular and organismal level is inadequate.  Basic information is also needed on the sources of infection (i.e., water, carrier fish, birds), modes of transmission (i.e., vertical from mother to offspring or horizontal from fish to fish), routes of entry (e.g., nares or gills), mechanisms of pathogen virulence and host response.  The lack of in vitro and in vivo models to investigate mechanisms of pathogenesis and virulence is hindering a better understanding of disease mechanisms.

Goals

1.      Develop challenge models in the laboratory that reflect on farm conditions to assess pathogenesis of disease.

2.      Develop in vitro methods to determine mechanisms of pathogenesis.

3.      Develop basic information on the sources of infection, modes of transmission, routes of entry, virulence mechanisms and host response to economically important infectious and non-infectious diseases.

4.      Discover novel natural product-based compounds for use in managing diseases.

Approaches

1.      Develop in vitro and in vivo models for parasites, viruses, bacteria and toxin investigations.

2.      Conduct microbiological, parasitological and epidemiological research to identify the sources of infection, modes of transmission, routes of entry, virulence mechanisms and host response.

3.      Conduct pathological research to determine mechanisms of pathogenesis and virulence.

4.      Conduct bacterial bioassays to screen natural and natural product-based compounds to identify novel, selective disease control agents.

Outcomes

• In vitro and in vivo models for parasites, viruses, and bacteria investigations will be developed. 
• The sources of infection, modes of transmission, routes of entry, virulence mechanisms and host response to infectious and noninfectious aquatic animal pathogens will be identified. Basic information on the mechanism of pathogenesis will be discovered. 

ARS Locations

• Auburn, AL
• Stuttgart, AR 
• Leetown, WV 
• Orono/Franklin, ME 
• Oxford,MS 

e.  Epidemiology

Epidemiology by definition is the science that deals with the incidence, distribution and control of disease in a population.  Fish farmers have suggested that epidemiology is needed to solve aquatic animal health problems on the farm.  Many times aquatic animal farmers do not or are not able to identify where all the fish or animals stocked “go”.  For example catfish farmers cannot account for approximately 70 % of their fish at time of harvest.  Studies need to address and/or identify the risk factors controlling the presence or absence of disease.  Use of epidemiology will allow for the identification of the problem areas that can be addressed by health management plans and/or cost effective control strategies (i.e., vaccines and medicines). 

Goals

1.      Develop methods to assess risk factors associated with the economically important pathogens of aquatic animals

2.      Carry out basic epidemiology studies to identify disease prevalence, incidence, sources and origin of economically important aquatic animal pathogens.

3.      Establish estimates of the economic impact of various pathogens on aquatic animal production. 

Outcomes

• Identification of major risk factors found in aquaculture production systems. 
• The prevalence, incidence, source and origin of economically important pathogens will be determined. 
• The estimated costs of diseases in aquatic animal production in different types of aquaculture systems will be determined. 

ARS Locations

• Auburn, AL 
• Leetown, WV 
• Stuttgart, AR

f.  Microbial Genomics

There is a critical need to obtain a better understanding of the molecular basis by which microbial pathogens cause disease in and interact with their hosts.  Whole-genome sequencing is a powerful method for rapidly identifying all of the genes of a microbe and serves as the basis for future functional analysis of the newly discovered genes.  Large-scale analysis of the microbial pathogen’s genome will identify novel antigens, biochemical pathways, and virulence mechanisms that are important for pathogen survival, pathogenesis and immunity.  In the future, genomic research will provide the basis for designing new and effective vaccines, medicines and diagnostic reagents to help prevent and control infectious diseases. Presently, no whole-genome of an aquatic animal pathogen has been sequenced.

Goals

1.      Increase the amount of available genetic information of aquatic animal pathogens (virus, bacteria and protozoa).

2.      Develop and/or adapt bioinformatic tools to properly process the information generated.

3.      Apply this new genetic information to functional genomic approaches in order to correlate sequence with gene function.

Approaches

1.      Construct genomic libraries using high-throughput sequencing of genomes of virus, bacteria or protozoa that are pathogenic for aquatic animals.

2.      Sequences will be combined into a whole genome shotgun assembly and organized using the appropriate bioinformatic tools. This assembly will be integrated with existing resources (e.g., expressed-sequence tags (ESTs).

3.      Make the data set publicly available via web-based tools and interfaces.

Outcomes

• Genomic sequence information on genes important in pathogenesis and virulence will be generated. 
• Knowledge of functional genomics of pathogenesis and virulence will be realized. 
• Genes and gene products useful in the development of diagnostic tests, vaccines and medicines that can reduce or eliminate the impact of these pathogens in aquaculture will be identified. 

ARS Locations

• Auburn, AL 
• Stuttgart, AR 
• Leetown, WV 

g.  Aquatic animal health management

More information is needed on fish responses to different stressors.  Husbandry techniques need to be developed that minimize the stress of the aquatic animals in production systems (i.e., information on handling and transport, stocking densities, water qualities).  Environmental factors including toxicogenic algae that effect animal well-being also need to be addressed.  This is especially important because water quality is important for aquatic animal well-being.  More information is needed on the sources of current and potential pollutants that may enter aquaculture production systems and negatively impact overall health of the aquatic animals.  Basic information is needed for development of biosecurity plans to prevent the spread of disease in aquaculture production systems, between wild and cultured fish, and between geographically isolated locations. 

Goals

1.      Improve health management practices currently used in aquaculture and at hatcheries.

2.      Identify factors of intensive aquaculture operations that can enhance animal well-being and decrease stress.

3.      Develop biosecurity plans to curtail the spread of diseases between geographical locations and between cultured and wild fish populations. 

Approaches

1.      Conduct basic and applied research to enhance health management plans in production systems.

2.      Conduct basic research on behavior, husbandry and environmental factors that affect aquatic animal well-being.

3.      Conduct basic and applied biosecurity research for prevention and control of infectious and non-infectious disease in targeted species. 

Outcomes

• Cost effective health management plans will be developed and employed by aquaculturists. 
• Factors that affect animal well-being will be identified. 
• Basic health management practices useful for the development of biosecurity plans for aquaculture production systems will be realized. 

ARS Locations

• Auburn, AL 
• Stoneville, MS 
• Stuttgart, AR 
• Leetown, WV
• Orono/Franklin, ME