National Aquatic Animal Health Laboratory System

Achieving Excellence in Regulatory Science - ISO 17025 Laboratory Accreditation

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The role of a NAAHLS National Reference Laboratory is to function as a centre of expertise by developing internationally recognized standardized diagnostic tests for designated pathogens.

NAAHLS provides quality diagnostics, targeted research, and sound scientific advice to support aquatic animal health in Canada.

Internationally recognized terrestrial and aquatic animal health programs around the world are underpinned by credible national laboratory systems which deliver accurate, reliable, and consistent test results for pathogen detection based on the international standards of the World Organisation for Animal Health (OIE). This capability, strengthened by continuing commitments to technology development and targeted research, provides participating countries with a sound scientific foundation to protect their animal populations from the introduction of pathogens, a responsive integral domestic disease management program, and enables participating countries to defend their certification of exported animals/products.

DFO’s National Aquatic Animal Health Laboratory System (NAAHLS) was designed with this capability in mind and is comprised of four laboratories across Canada:

  1. the Pacific Biological Station – Aquatic Animal Health Laboratory (Nanaimo, BC) (PBS-AAHL), Nanaimo, BC;
  2. the Freshwater Institute – Aquatic Animal Health Laboratory (Winnipeg, MB) (FWI-AAHL), Winnipeg, MB;
  3. the Gulf Fisheries Centre – Aquatic Animal Health Laboratory (Moncton, NB) (GFC-AAHL); and
  4. the Gulf Biocontainment Unit - Aquatic Animal Health Laboratory (GBU-AAHL).

While the first three labs provide diagnostic testing and research, GBU-AAHL is a level 3 containment laboratory capable of performing research on foreign exotic pathogens. Each diagnostic testing lab is responsible for conducting pathogen testing of wild and farmed finfish, molluscs, and crustaceans for the National Aquatic Animal Health Program (NAAHP) and the Fish Health Protection Regulations (FHPR). Both the PBS and GFC routinely conduct pathogen testing to support the movement of finfish, molluscs, and crustaceans for the National Code on Introductions and Transfers of Aquatic Organisms. The NAAHP currently has three wild fish and shellfish pathogen surveillance programs (Surveillance Program in DFO) underway in British Columbia (Pacific salmon and shellfish) and Québec (freshwater fish) with DFO NAAHLS conducting the diagnostic testing. A separate initiative for diagnostic testing for the BC aquaculture industry is conducted outside NAAHLS through Fisheries and Aquaculture Management Division.

Science and technology development are integral to Canada's performance in validating diagnostic detection methods for significant fish pathogens. Scientists and technicians at the NAAHLS laboratories enable DFO to fulfill its responsibilities for conducting diagnostic testing, research to improve detection techniques and disease controls, and targeted research. Each NAAHLS diagnostic lab is designated as a national reference lab for specific pathogens. While other NAAHLS labs may undertake screening or surveillance for these pathogens, the validation of any positive test results must be done by the responsible national reference lab to confirm positive test results for that pathogen. The NAAHLS labs do not test for pathogens of human health concerns; this is the role of the Public Health Agency of Canada.

The NAAHLS supports targeted NAAHP research priorities, which are established in collaboration with CFIA through the Centre for Aquatic Animal Health Research and Diagnostics (CAAHRD). This research can include, but is not limited to, the development and validation of new diagnostic test methods for the detection of infectious disease agents in aquatic animals, research on high priority pathogens, and the susceptibility of aquatic animals to specific pathogens.

Other programs that fund aquatic animal health research and/or require diagnostic testing can benefit from NAAHLS scientific expertise of DFO scientists and technicians, as well as laboratory facilities, such as the Program for Aquaculture Regulatory Research and the Aquaculture Collaborative Research and Development Program. DFO also conducts non-regulatory diagnostic testing for the Salmonid Enhancement Program under the Habitat and Enhancement Branch.

Pacific Biological Station

Pacific Biological Station – Aquatic Animal Health Laboratory (Nanaimo, BC)

The Pacific Biological Station located in Nanaimo, BC.
Source: Fisheries and Oceans Canada

The Pacific Biological Station (PBS) in Nanaimo, BC was established in 1908 and is the principal research centre for British Columbia, the Northeast Pacific Ocean, and the Western Arctic. It is the oldest fisheries research centre on the Pacific coast and forms part of a network of major scientific facilities operated by Fisheries and Oceans Canada. Since 1960, PBS provided diagnostic services to support many different clients and programs including the Federal Hatchery system under the Salmonid Enhancement Program, DFO Pacific Region research initiatives, First Nations, the public, and more recently, the National Aquatic Animal Health Program.

The NAAHLS lab at the PBS have the capability to employ a wide variety of test methods to detect pathogens, such as tissue culture, virology, histology, and molecular biology. A key to providing reliable and consistent results lies in the validation of these techniques in conjunction with a strong Quality Assurance program. Researchers assist in the technology transfer of the detection techniques of national reference laboratory pathogens to other DFO NAAHLS laboratories and also participate in the development of containment and quarantine standards.

NAAHLS Research at DFO's Pacific Biological Station

Aquatic animal health research at DFO’s Pacific Biological Station (PBS) focuses on pathogens of relevance to wild and cultured finfish and shellfish within the Pacific Region. Research also provides support for the National Aquatic Animal Health Program (NAAHP). The aquatic animal health laboratories employ a wide variety of test methods to detect pathogens, such as tissue culture, parasitology, bacteriology, virology, histology, and molecular biology. A key to providing reliable and consistent results lies in the validation of these techniques in conjunction with a strong Quality Assurance program. Researchers assist in the technology transfer of the detection techniques for those pathogens for which they are a reference laboratory to other DFO laboratories and also participate in the development of containment and quarantine standards. Scientists at PBS also undertake aquaculture regulatory research (PARR program) and collaborative research in support of aquaculture (such as DFO’s Aquaculture Collaborative Research and Development Program). In addition, genomics technologies are applied to better understand pathogen diversity and host-pathogen interactions in finfish and shellfish (Genome BC and Genomics R&D Initiative).

NAAHLS Researchers at DFO's Pacific Biological Station

Freshwater Institute

Freshwater Institute – Aquatic Animal Health Laboratory (Winnipeg, MB)

The Freshwater Institute (FWI) located in Winnipeg, Manitoba serves as the regional headquarters for DFO’s Central and Arctic Region and is home to a fish health program that has operated since 1973. The FWI aquatic animal health lab is responsible for performing diagnostic testing using a number of different methods: virology, serology, biotechnology and genetics-based testing as well as classical microbiological and biochemical assays.

Quality diagnostic services and aquatic animal disease research are provided in support of the following:

  • Fish health certification services under the authority of the Fish Health Protection Regulations to regional aquaculture facilities
  • National Aquatic Animal Health Program (NAAHP)
  • Fish health monitoring services to regional/provincial fish hatcheries in support of wild stock enhancement activities
  • Regional fish disease surveillance and survey of wild populations
  • General public

NAAHLS Research at DFO's Freshwater Institute

DFO analyst is analysing results of a qPCR run.
Source: Fisheries and Oceans Canada.

The FWI scientists and staff at the aquatic animal health laboratory are engaged in a number of scientific research initiatives related to reportable, notifiable, or other diseases that impact the health of wild and farmed finfish. Projects are designed to identify emerging viruses in finfish, particularly in endangered species, and investigate the distribution and genetic relatedness of these viruses among wild fish populations. Addressing these specific knowledge and technology gaps may lead to a better understanding of the biology of these viruses and their impact on wild populations of fish.

A new type of genetic-based assay – referred to as quantitative polymerase chain reaction (qPCR) - has become widely used and accepted in modern molecular diagnostics. Dr. Clouthier is leading studies to develop new or modified qPCR assays capable of detecting IPNv or KHv. The assays are being evaluated as fit for purpose through validation studies that establish the analytical and diagnostic performance of each test method. These assays are highly sensitive, specific, and fast. They recognize isolates of IPNv and KHv commonly found in North America and enable samples to be screened within several days rather than the three weeks currently required for completion of classical cell culture techniques. These new assays are part of a suite of diagnostic assays that are being used within NAAHLS laboratories for screening aquatic animals for infectious disease agents.

Viral Pathogens in Native and Colonizing Fish species in Arctic Ecosystems

The long term goal of this project is to assess the prevalence, distribution, and emergence of viral pathogens in native and colonizing fish species in arctic ecosystems and to establish a normative baseline for future monitoring activities. In addition, understanding the impact that key global drivers, such as climate change, have on infectious diseases of fish will facilitate the development of a systems approach for managing fish health in the region. The results will lead to a better understanding of where surveillance and risk mitigation efforts need to be focused to reduce the threat of disease emergence due to climate change in the western Arctic.

Addressing Disease Risks of Manitoba Lake Sturgeon

The aim of this research project is to generate a body of knowledge that can be used to instruct the design and development of an infectious disease management plan for Lake sturgeon in Manitoba. The objectives are fourfold: 1) analysis to identify the virus and sequence its genome, 2) development and validation of molecular detection methods capable of recognizing the virus, 3) spatial and temporal distribution of the virus and its genetic relatedness within and among Lake sturgeon populations considered by COSEWIC to be endangered in Canada, and 4) risk factor studies to assess virus prevalence in conjunction with virus infection and transmission patterns in a Lake sturgeon hatchery setting.

NAAHLS Researchers at DFO's Freshwater Institute

Gulf Fisheries Centre

Gulf Fisheries Centre – Aquatic Animal Health Laboratory (Moncton, New Brunswick)

The Gulf Fisheries Centre (GFC) located in Moncton, New Brunswick, is the regional headquarters for the DFO Gulf Region, at the DFO’s Gulf regional headquarters. The aquatic animal health laboratory at GFC provides quality diagnostic testing and aquatic animal pathogen research in support of the following:

  • Fish health certification of aquaculture facilities under the authority of the Fish Health Protection Regulations
  • National Aquatic Animal Health Program (NAAHP)
  • Shellfish health testing in support of Introductions and Transfers and harvesting
  • Fish health testing in support of wild stock enhancement activities
  • Testing to determine wild shellfish and finfish mortalities

The aquatic animal health laboratory at GFC is operated by the Aquatic Animal Health Section within the Aquatic Health Division of the Science Branch. The section includes three groups, each responsible for the delivery of different diagnostic tests: the Fish Health Unit, the Shellfish Health Unit, and the Molecular Biology Unit. The laboratory is responsible for the development and validation of new diagnostic tests for the detection of pathogens in aquatic animals. In addition, scientists and researchers at the lab work to increase the knowledge on host-parasite interactions, species susceptibility to pathogens, pathogen strain differentiation, and disease control mechanisms.

Fish Health Unit

The Fish Health Unit (FHU) has tested fish on Canada’s East Coast since 1975. The unit is responsible for performing various tests for the detection of fish pathogens. The most common tests performed by the group are necropsy, virus isolation, and bacteriology. The FHU provides testing under the Fish Health Protection Regulations for over 30 aquaculture facilities located in various parts of Québec, New Brunswick, Nova Scotia, Prince Edward Island, and Newfoundland. The FHU also performs testing to support wild stock enhancement of salmonids in New Brunswick and Nova Scotia.

Shellfish Health Unit

The Shellfish Health Unit (SHU) focuses on disease agents of molluscs. The unit performs necropsies and histopathological analysis using light microscopy, and sometimes other tests, such as bacteriology, for the detection of pathogens which may impact the health of shellfish. The SHU has led an oyster health monitoring program in the Maritime Provinces for over a decade.

Molecular Biology Unit

Scientists at the GFC have had molecular diagnostic capability since 2001 and they currently conduct testing in conjunction with the fish and shellfish unit. The Molecular Biology Unit specializes in using polymerase chain reaction (PCR) to detect specific pathogens within a sample. The group uses quantitative PCR, also known as qPCR, to detect the RNA (for certain viruses) or DNA of a pathogen. The test is sometimes used to confirm a test result obtained using a different diagnostic test, but can be used as a screening test in its own right. The group also has other molecular tools at its disposal.

NAAHLS Research at DFO’s Gulf Fisheries Centre

Aquatic animal health research at GFC focuses on pathogens relevant to wild and cultured finfish and shellfish within the Atlantic Region of Canada and supports the National Aquatic Animal Health Program (NAAHP) by conducting research to develop and improve diagnostic processes. As part of the National Aquatic Animal Health Laboratory System (NAAHLS), GFC employs a wide variety of test methods to detect pathogens, such as tissue culture, parasitology, bacteriology, virology, histology, and molecular biology. A key to providing accurate, reliable, and consistent test results lies in the validation of detection techniques in conjunction with a strong Quality Assurance program. Researchers at all NAAHLS labs assist in the technology transfer of detection techniques for those pathogens for which they are a reference laboratory to other DFO laboratories. GFC researchers also undertake aquatic animal health research to support aquaculture (e.g., Aquaculture Collaborative Research and Development Program). In addition, genomics technologies are applied to better understand pathogen diversity, host-pathogen interactions in finfish and shellfish, such as the response of animals to disease, and how various isolates affect animals differently.

Parasites affecting Atlantic aquaculture development

NAAHLS Researchers at DFO’s Gulf Fisheries Centre

Gulf Biocontainment Unit

Aquatic Animal Health Gulf Biocontainment Unit

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Gulf Biocontainment Unit – Aquatic Animal Health Laboratory (Charlottetown, PEI)

The Gulf Biocontainment Unit – Aquatic Animal Health Laboratory (GBU-AAHL) is located in a Canadian Food Inspection Agency (CFIA) laboratory in Charlottetown, P.E.I. and is affiliated with DFO's Gulf Fisheries Centre. The GBU-AAHL contributes to research and diagnostic test development, scientific advice, and testing related to high-risk pathogens. In 2009, the state-of-the-art GBU-AAHL received official certification as a level three (L3) containment laboratory for live aquatic animal work making it one of a few aquatic animal biocontainment laboratories in the world that can undertake studies with exotic and serious aquatic animal disease causing agents. This certification was a critical step toward enabling DFO to safely conduct research into virtually any aquatic animal disease or pathogen, including the ability to study aquatic animal disease interactions in a controlled environment and to investigate new or emerging diseases. It is the only NAAHLS facility approved for live trials with exotic pathogens.

Diagnostic tests developed and validated by GBU-AAHL are ultimately transferred to the three diagnostic System laboratories of the NAAHLS where they are integrated into routine diagnostic use.

The GBU-AAHL lab is a modern facility with sophisticated back-up systems to support lab bench work, a variety of different animal holding systems and extremely stringent sterilization processes for lab waste water and lab-generated waste material. Experimental challenge models developed in the GBU-AAHL facility lab are useful when there is no source of naturally affected animals available for use in test development and validation. Animal holding facilities can operate a variety of conditions required for optimal animal care including freshwater though to full saltwater systems at very cold to warm environments (5 – 35 °C) with controlled lighting and closely monitored (and adjustable) water quality parameters. Shellfish, finfish, and bivalves can be held at GBU-AAHL.

For more information: Canadian Food Inspection Agency Containment Standards for Facilities Handling Aquatic Animal Pathogens

Biocontainment

All waste-water at the Gulf Biocontainment Unit – Aquatic Animal Health Laboratory biocontainment lab is stored in sealed tanks before being sterilized in specialized large capacity pressure vessels or cookers (above) using high temperature and pressure treatment prior to discharge. No chemicals are used in this process.
Source: Fisheries and Oceans Canada.

Manipulation of infectious materials takes place in specialized containment structures such as this Biological Safety Cabinet (BSC), located within a containment laboratory. Working within a BSC enhances the stringent biocontainment already present within the room through the combination of operational and physical strategies including the use of standard operating procedures followed by trained staff, sophisticated air flow patterns, physical barriers and fine-filtration of air within the cabinet.
Source: Fisheries and Oceans Canada.

‘Biocontainment’ refers to the use of specialized facilities, equipment, and procedures that create multiple levels of barriers that prevent release of infectious material while permitting work with live pathogens. ‘High level’ biocontainment uses sophisticated physical strategies such as air flow and filtration, sterilization processes for water and lab waste and specialized design features of floors, walls and ceilings in complementary and redundant arrangements that assist in preventing the escape of potentially harmful agents to the outside environment. Physical barriers work in concert with specific protocols that are followed when staff, supplies, animals, samples and waste material enter and leave containment.

High-level biocontainment is a lay term commonly applied to level three (L3) and level four (L4) containment labs. Level three (L3) biocontainment designation for facilities working with aquatic animal pathogens is (‘AQC3’) issued by the CFIA office of Biohazard Containment and Safety. Biocontainment certification is based on the guidelines provided in the document Containment Standards for Facilities Handling Aquatic Animal Pathogens. AQC3 (in vivo) enables research with high risk pathogens in live animals and allows for the preparation of inactivated (no longer infectious) samples for further study at the laboratory bench level in a safe manner. L3 laboratories that are used for live animal work are considerably more complex in terms of specialized requirements related to the movement of pathogens, animals, and people within the facility, disinfection procedures, and waste treatment compared to labs doing non-animal bench work. The DFO NAAHLS labs at the Pacific Biological Station, the Freshwater Institute, and the Gulf Fisheries Centre are all level 2 containment labs.

"We are always concerned with preventing the escape of pathogens that we work on here, thus both the entry and exit procedures for staff, equipment and supplies are very stringent," says Dr. Philip Byrne, section head of the Gulf Biocontainment Unit – Aquatic Animal Health. "We have back-ups for our back-up systems, and we treat both the water coming in and waste water using various disinfection and sterilization processes."

NAAHLS Research at DFO’s Gulf Biocontainment Unit – Aquatic Animal Health Laboratory

In order to assist with the effort in satisfying trading partners that Canadian exports of crustacean products (especially lobster) are free of serious exotic disease-causing agents, researchers at the GBU-AAHL facility carry out research using shrimp and lobster to develop testing procedures and investigate the susceptibility to selected disease agents. It is important to note that when it comes to trade in animal (and plant commodities) the mere presence of an unwanted disease agent, whether or not it is actually causing disease at that moment, can become a serious trade issue.

Finfish test development and disease susceptibility

In addition to the crustacean disease agents being looked at GBU-AAHL, several serious finfish viral diseases have also been investigated. Several viral disease agents that are considered emergent disease entities in Canadian waters or exotic to Canadian territory include Viral Hemorrhagic Septicemia (VHS) and Salmon Pancreas Disease virus (SPDv), respectively. Various strains of VHS have been reported from across Canada in fresh and salt water environments and infect a wide variety of fish species. SPDv causes disease in Atlantic salmon. Strains from both of these viral agents have been investigated using salmon and trout experimental models at the Charlottetown lab. These projects are in support of NAAHP-led projects involving other DFO facilities and research scientists. Future experimental finfish host-pathogen model systems that will be established at GBU-AAHL include work with the following exotic disease causing agents: Red Sea Bream Iridovirus Disease (RSIVD), Oncorhynchus masou virus (OMv) and Epizootic Haematopoietic Necrosis virus (EHNv).

Post-mortem services and molecular analysis

Not all research and test development involves live animal projects. The GBU-AAHL facility lab is also well equipped for bench-level molecular analysis and post-mortem services, both operated within biocontainment-designated areas in the building. Pathology expertise complements work done at the molecular level and is a usual starting point for investigations into unusual disease presentations that may not be immediately recognizable or detectable by current molecular tests.

NAAHLS Researchers at DFO’s Gulf Biocontainment Unit - Aquatic Animal Health Laboratory

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