Speaker information in order of agenda appearance...

SESSION 1:  Pathogens and disease in salmon: current knowledge and methods of study


Title of presentation:  Novel approaches for the monitoring and modeling of infectious diseases in salmon populations

Abstract: Diseases may have a devastating impact in wild populations, cause substantial decline in abundance or even threaten conservation efforts and biodiversity. A better understanding of disease dynamics, risk factors and transmission patterns in a population is critical to inform the design and implementation of more cost-effective prevention, mitigation and control strategies. This can be in part accomplished with monitoring programs that capture information about the demographics and health status of the study population as well as about environmental and other potential contributing factors. However, data collection and modeling disease dynamics in wild populations and, particularly in aquatic organisms, is challenging as many times we have hidden disease states, imperfect disease detection methods and missing data. It is also challenging to estimate the contact rates and other parameters to more realistically simulate disease dynamics. In this talk we will discuss the foundations and challenges of current monitoring and modeling approaches of wild populations, with particular examples in salmonids, as well as we will describe the opportunities to advance in the study of disease dynamics by implementing novel methodological approaches and new tracking technologies.

We will also discuss the need to use monitoring systems in combination with disease transmission models, risk assessment, economic models and other quantitative approaches to better inform decision making and increase awareness of different stakeholders and the general public regarding the need to more actively participate in the monitoring, prevention and control of diseases in wild populations.

Bio: Beatriz Martínez-López, D.V.M, M.P.V.M., Ph.D., is Associate professor of infectious disease epidemiology at the Department of Medicine & Epidemiology, Veterinary School, UC Davis and Director of the Center for Animal Disease Modeling and Surveillance (CADMS) since January 2014.  Dr. Martínez López research is focused on the development and application of epidemiological tools for supporting more cost-effective and risk-based surveillance and control strategies. She has been primarily working on epidemiological modeling and risk assessment of the evolution/spread of infectious diseases affecting domestic and/or wild animal populations such as foot-and-mouth disease, African Swine Fever, avian influenza, Rift Valley Fever, Porcine Reproductive and Respiratory Syndrome, West Nile or bovine tuberculosis, among others. Many of those diseases are considered to be emerging or re-emerging due to globalization, climate and land use changes. Currently she is also working in diseases affecting aquatic animals, mainly those related with shrimp and salmon farming industry. Since January 2014 when she assumed the direction of CADMS, she is leading the continuing development and implementation of the Disease BioPortal (http://bioportal.ucdavis.edu/), an operational, secure web-based platform system intended for real-time routing, sharing, analyzing, visualizing and modeling of Big Data to better prevent and control infectious diseases.


Title of presentation:  Aquatic Animal Health Program at UC Davis: What we do and why we do it….

Esteban Soto, MSc, DVM, PhD, Dipl. ACVM, CertAqV 

Associate Professor of Aquatic Animal Health

Department of Medicine & Epidemiology

School of Veterinary Medicine

University of California-Davis 
2108 Tupper Hall
Davis, CA 95616-5270

Abstract: In recent years, the field of aquatic animal medicine has grown exponentially. The field is tremendously diverse and include aquaculture of aquatic animals for ornamental and human consumption; as well as conservation and aquarium programs. Moreover, aquatic animals are becoming more and more used as models to study human and animal diseases. Pet fish are the most common pet species owned in America with over 105 million fish owned in over 12.3 million households. Aquaculture is one of the world’s fastest developing food production sectors. The industry has experienced rapid growth in recent years as global catches from wild fisheries plateau, reach maximum sustainable yields or have declined since the 1980’s. Aquaculture is now expected to produce over half the fish consumed by humans and intensification of fish production is expected to surpass any growth in global wild fisheries in the near future. With this recent growth and emphasis on the field of aquatic animal medicine, knowledge of fish diseases and pathogens has also expanded drastically.  During the last two decades, a multitude of bacterial, fungal, parasitic and viral microorganisms have been identified in wild and captive fish populations. The goal of the UC Davis School of Veterinary Medicine Aquatic Animal Health program is to better understand the pathogenesis of important infectious diseases of wild and aquatic animals, and to develop strategies to protect animals from these diseases. In this presentation, a general overview of our program and current research will be presented.

Bio: Dr. Esteban Soto received his veterinary degree from Escuela de Medicina Veterinaria, Universidad Nacional, Costa Rica in 2005. He then completed a Master’s degree program in Veterinary Science/Aquatic Pathobiology at Mississippi State University in 2007, and a PhD in Pathobiological Sciences from Louisiana State University in 2010. He served as an assistant and later as an associate professor of Veterinary Bacteriology and Mycology at Ross University-School of Veterinary Medicine from 2010-2015, when he joined the Department of Medicine and Epidemiology and Companion Exotic Animal Medicine & Surgery Service at UC Davis. Dr. Soto became a certified fish pathologist by the American Fisheries Society-Fish Health Section in 2010, board certified by the American College of Veterinary Microbiologists with subspecialties in Veterinary Bacteriology and Mycology and Veterinary Immunology in 2013, and certified as an Aquatic Veterinarian by the World Aquatic Veterinary Medical Association in 2015. His main research interests are to understand the pathogenesis of important infectious diseases of wild and aquatic animals, and to develop strategies to protect animals from these diseases.

SESSION 2: West Coast Case Studies: Monitoring and managing for disease


Title of presentation: Ceratonova shasta and Parvicapsula minibicornis infection in Sacramento and Feather River juvenile Chinook salmon: Spatial, temporal, and river condition influence on disease severity

J.Scott Foott*, Jennifer Jacobs, Ron Stone, Kim True,  Ann Voss, and Alana Imrie1

U.S. Fish and Wildlife Service, CA-NV Fish Health Center, Anderson CA

1 California Department of Water Resources, Oroville, CA

Abstract: Ceratonova (previously Ceratomyxa) shasta and Parvicapsula minibicornis are endemic myxozoan parasites of salmonid fish in the Pacific Northwest and can have significant impacts on juvenile health. Survey and sentinel fish exposure data from 2014 – 2017 in both the Feather and Sacramento River will be discussed in context of seasonality, zones of infectivity, and river conditions influence on disease severity. Considerations for disease surveys of juvenile salmonids will also be discussed.


  • A UC Davis graduate (PhD Comparative Pathology, 1989)
  • Fish Pathologist with Idaho Fish& Game (1987-1989) and USFWS project leader at CA-NV Fish Health Center since 1990
  • FHC has conducted cooperative disease surveys on juvenile salmonids since 1991 in the Trinity, Klamath, and Central Valley watersheds.
  • FHC conducts a variety of wetlab studies on disease and physiology on salmonids, smelt, and suckers.
  • FHC has conducted a wider variety of surveys on multiple fish species under the USFWS National Wild Fish Survey since 1997


Title of presentation: California Department of Fish and Wildlife Fish Health Laboratory Health Monitoring Program for the state hatchery system

Presentation summary-Disease in CA hatcheries: overview of what pathogen or disease screening is done at state hatcheries

Abstract: The mission of the California Department of Fish and Wildlife (CDFW) Fish Health Laboratory (FHL) Program is to monitor fish health, diagnose disease and recommend treatments for fish in CDFW hatcheries and to monitor and investigate wild fish health issues in California's waters. Over the years, the FHL's responsibilities have increased to include many other areas, all focused towards the protection of the state’s fish resources.  This presentation will provide a brief overview of the program’s responsibilities and will review the CDFW hatchery fish health program.

Bio: Dr. Adkison is the Statewide Fish Health Coordinator for the California Department of Fish and Wildlife Fish Health Program. He has been a research scientist for over 30 years studying animal disease and immunology.  He has a B.S. in Biochemistry, a M.S. in Comparative Pathology and a Ph.D. in Microbiology from U.C. Davis.  His focus on fish research began during his post-doctoral fellowship at Oregon State University, investigating the effects of carcinogens on the immune system using rainbow trout as his animal model.  Following his Post-Doc at Oregon State, in 1993 he returned to U.C. Davis to study fish disease and immunology in the Aquatic Animal Health Laboratory in the UC Davis School of Veterinary Medicine.  In 2004 he accepted a position with the California Department of Fish and Game as a Fish Pathologist, and in 2007 he assumed the role of the Statewide Fish Health Coordinator position that he holds today.


Title of presentation: Monitoring a fish pathogen to inform management and models: A three-pronged program for Ceratonova shasta in the Klamath River

Sascha L. Hallett*, Richard A. Holt, Julie D. Alexander, Ryan Craig, Stephen D. Atkinson, Charlene N. Hurst, R. Adam Ray, and Jerri L. Bartholomew

Department of Microbiology, 226 Nash Hall, Oregon State University, Corvallis, Oregon, USA 97331; halletts@oregonstate.edu

Abstract: Ceratonova shasta (formerly Ceratomyxa shasta) causes enteronecrosis in juvenile salmonids in the Pacific Northwest of North America and is associated with population-level impacts in the Klamath River. This myxozoan parasite cycles between two hosts and two spore stages: actinospores develop in freshwater polychaete worms, then invade salmonids in which they form myxospores. In response to the high prevalence and severity of C. shasta-infection in Klamath salmonids, we developed a parasite monitoring program to track C. shasta’s spatial and temporal abundance. Our three-pronged approach captures each part of the life cycle and includes sentinel fish exposures, invertebrate host collection and waterborne parasite sampling. In 2006, we established 5 mainstem index sites, which span 240 river kilometers, and 4 sites in tributaries. Whereas polychaete sampling occurs quarterly (once each season), fish exposures occur primarily during juvenile outmigration, and water samples are collected weekly year round. Each facet of the program provides unique but complementary data. Sentinel fish provide metrics of prevalence of infection and disease severity (percent mortality and time to death). Polychaete sampling provides host density and prevalence of infection data. Direct, regular measurement of waterborne spores provides higher resolution surveillance and is a pragmatic alternative to host sampling, and facilitates semi-real-time reporting via weekly, online updates. In addition, our decadal dataset will aid identification of the primary biotic and abiotic drivers of host-C. shasta interactions in this system. Long-term monitoring of C. shasta has revealed significant variation associated with parasite abundance in water, and prevalence and severity of infection in its hosts among the 10 years. For example, in 2015 mortality in Chinook sentinel fish was a record 90.5% and spore abundance in water samples was 25 times higher than the previous year, and an order of magnitude higher than the previous highest level of ~100 spores/L in 2007-9. These data are informing model development (epidemiological and predictive) and host management strategies (e.g. pulse flow events). We identified disease thresholds for Chinook and coho salmon of 10 and 5 spores/L of their specific C. shasta ITS1-genotype, respectively. In 2014, when our real-time monitoring data parasite levels surpassed these thresholds, water was released from Iron Gate Dam in a ‘pulse flow event’ in an effort to reduce disease severity in outmigrating salmonids. The overarching management goal for the system is to reduce salmonid mortality below 40%.

Karuk and Yurok tribal biologists assisted with water sample collection and filtering.

Bio: Dr. Sascha Hallett is a Senior Research Associate in the Department of Microbiology at Oregon State University. She is a fish parasitologist who focuses on myxozoans (taxonomy, life cycles, ecology, epidemiology).

Dr. Hallett undertook her PhD in marine parasitology at the University of Queensland, Australia, and was then awarded an Alexander von Humboldt Research Fellowship at the University of Munich, Germany. Afterwards, she joined Dr Jerri Bartholomew’s lab at OSU where she has been studying myxozoan parasites of the Pacific Northwest. Her research there has included fish and worm susceptibility experiments (field and lab components), molecular assay development and detection of parasites in environmental water samples.

Dr. Hallett has been integral to the collaborative development of a comprehensive monitoring program for Ceratonova shasta in the Klamath River. Specifically, she developed an approach for direct sampling of waterborne stages to track the spatial and temporal abundance of the parasite to inform management strategies and model development.

Dr. Hallett teaches an online parasitology course and on-campus fish disease lectures and labs. She has contributed to > 40 journal articles and written several book chapters. She has reviewed manuscripts for 18 different journals and she is on the editorial board of the Journal of Aquatic Animal Health and Parasitology Research.


Title of presentation: Metrics that matter: ensuring that monitoring programs inform relevant demographics, and using multiple lines of (potentially incomplete) evidence to summarize the state of science for decision makers

Abstract: Monitoring programs are established for a variety of purposes, and for aquatic diseases these programs often track both environmental factors relating to infection and summaries of impacts to species of concern.  However, even if the monitoring programs are run concurrently, they might not provide estimates of disease risk or infection commensurate with the target population.  In this talk, we demonstrate how potential problems can arise, and an example of monitoring realignment to capture metrics relevant to the population.  We also discuss how an effort to pull information from multiple lines of evidence was used to inform decision makers.

Bio: Nicholas Som is a statistician working for the US Fish and Wildlife Service, in the Arcata, CA Fisheries and Aquatic Conservation program. Most of his work covers salmonids from the Klamath and Trinity rivers. Since 2011, Nicholas has been heavily involved in research planning and statistical modeling of C. shasta dynamics in the Klamath Basin.


Title of presentation: The Integration of Science and Management to Control Disease on the Klamath River

Abstract: During 2002, more than 34,000 adult salmonid en route to their spawning grounds perished within the Yurok Reservation boundaries of the Lower Klamath River from outbreaks of Ichthyophthirius multifiliis (Ich) and Flavobacter columnare (Columnaris).  Klamath Basin juvenile salmonids have suffered from high rates of infection by the parasite Ceratonova shasta (C. shasta) during several years since 2005, when a consistent monitoring program was initiated, especially during the years 2014 and 2015, when prevalence of infection rates by C. shasta were 81% and 91% respectively.  These high rates of C. shasta infection were contributing factors to the recent collapse of the Klamath Fall Chinook population during 2016 and 2017. 

The prevalence of Ich and C. shasta can be linked, at least in part, to flow management.  In an effort to minimize the risk of another adult fish kill in the Lower Klamath River, the Bureau of Reclamation (BOR) augmented late summer/fall flows from Trinity Reservoir during seven years since the 2002 fish kill occurred.  Furthermore, an EIS was completed by the BOR in 2017 to provide augmented flows into the foreseeable future when deemed necessary to minimize the risk of another adult fish kill.

Following the high juvenile disease rates of 2014 and 2015, which substantially exceeded thresholds identified in the incidental take statement of the 2013 Biological Opinion for BOR’s Klamath Irrigation Project, the Yurok and Karuk Tribes requested the Arcata USFWS to summarize the best available science regarding C. shasta in the Klamath River.  USFWS summarized this science in four peer reviewed technical memoranda, which facilitated the use of this information by the Yurok, Karuk, and Hoopa Valley Tribes while developing a synthesis document (Measures to Reduce Ceratanova shasta Infection of Klamath River Salmonids: A Guidance Document) intended to provide guidance recommendations to managers regarding flow measures intended to minimize future juvenile disease outbreaks of C. shasta.  During subsequent litigation, a judge ordered reconsultation of the BiOp and implementation of three of the flow related measures identified in the synthesis document. 

Bio: Dave Hillemeier has been the Director of the Yurok Tribal Fisheries Department since 1999.  Prior to that he was a Senior Fisheries Biologist for the Tribe from 1995 – 1999.  Dave received his Master of Science degree, as well as a Bachelor of Science degree, from Humboldt State University.  Dave has worked in the Klamath Basin conducting fisheries related work since the mid-1980’s.  Dave oversees the Tribe’s Fisheries Department that employs 20 professionals (fisheries biologists, habitat biologists, a geomorphologist, and a civil engineer), and up to 30 fisheries technicians that work throughout the Klamath Basin to responsibly manage, conserve, and restore the Tribe’s fisheries resource.  Primary tasks of the Yurok Fisheries Department include management of the Tribe’s fishery, biological monitoring and research throughout the Basin, water management activities at the technical and policy levels, review of land management activities throughout the basin, and substantial habitat restoration activities throughout the Lower Klamath and Trinity River Basin.  Dave, along with other key Yurok staff, has been closely involved with the FERC relicensing, and now decommissioning, processes for the Klamath River dams since the traditional relicensing process began in 2001. 


SESSION 3: Science Information and Management


Title of presentation: Implications of Salmonid Disease Concerns to Operations at Army Corps Dams in the Columbia River Basin

Abstract: The US Army Corps of Engineers operates 12 dams as part of the Federal Columbia River Power System, eight of which form a continuous series of Army Corps dams on the lower Snake and Columbia rivers.  These dams not only form impediments to fish migration by their physical presence, but they also create reservoirs that slow fish movement, cause water temperatures to rise, and lead to increased predation mortality.  The Army Corps has taken measure to reduce the impact of dams on salmonid migration and survival by installing adult and juvenile fish passage systems.  In addition, several of these dams operate fish collection facilities that support fish transportation programs (barging and trucking) and fish condition monitoring programs.  The Smolt Monitoring Program is a joint partnership between federal, state, and private industries that evaluates and reports on the status of fish passing Army Corps dams, including passage numbers, size range, mortality, and health and condition.  The health and condition monitoring reports on signs of injury, predations marks, and indications of disease and parasites.  When disease detections increase, a suite of operations options may be exercised including changing fish barging patterns, immediate release of fish retained in raceways, efforts to reduce forebay temperatures, and increasing spill to encourage faster juvenile emigration.  Fish disease and condition monitoring provides critical data to guide water operations and fish transportation programs intended to reduce salmonid mortality associated with the presence of Army Corps dams.

Bio: “Towns” Burgess has nearly 20 years of experience in fisheries working in a variety of disciplines from population genetics of sharks in the Western Atlantic Ocean and habitat use of Gulf Sturgeon to floodplain restoration and salmon passage at dams.  He received a Bachelor’s Degree in Marine Biology from the University of South Carolina and a Masters and Doctorate in Fisheries from the University of Florida, where he investigated multi-trophic impacts of industrial discharge into the St. Johns River.  At his previous position, he was a supervisory biologist responsible for ensuring safe and efficient passage of salmon past Army Corps of Engineer Dams on the Snake River.  Currently, he is a fish biologist for the Bureau of Reclamation, where he works to reduce the impacts of Central Valley Project operations on ESA-listed fishes.


Title of presentation:  Integrative approaches for studying freshwater and marine fish diseases

Abstract: The fish health research program at the Western Fisheries Research Center (WFRC) includes a mix of basic and applied science focused on understanding the factors that control the distribution and severity of infectious diseases affecting both wild and hatchery fish. Much of our research focuses on improved understanding of the epidemiological features of aquatic animal disease including critical ecological factors that affect the host-pathogen relationship. Our research uses a combination of approaches including field epidemiology, controlled laboratory studies and modeling.  For instance, field molecular epidemiology of the salmonid virus – infectious hematopoietic necrosis virus (IHNV) – reveal interesting host patterns that are investigated using controlled laboratory experiments or spatial patterns that are explored with transmission models. In my talk, I will present several examples of how we use these approaches to study diseases of salmon and forage fish in the freshwater and marine environments.

Bio: Dr. Purcell is the Chief of the Fish Health Section at the Western Fisheries Research Center (WFRC) in Seattle, WA.  She earned her Ph.D. from the University of Washington and took a position at the WFRC after graduation.  Research at the WFRC focuses on infectious diseases of fish, molecular taxonomy and epidemiology of fish pathogens, ecology of fish diseases in wild populations and fish host defenses. The WFRC also provides technical assistance to federal, state and tribal fisheries agencies, including activities such as training, technology transfer and response to emerging fish pathogens.


Title of presentation:  Economics and farmed fish health management

Abstract:  Salmon production is Chile’s main aquaculture activity, with an export value of US$2.4 billion in 2008. Nonetheless, numerous issues, such as the exhaustion of natural resources and large-scale sanitary problems, may threaten long-term plans for sustainable development in this industry. The amount of diseases has increased steadily, and there are at least 15 different infectious agents currently recognized in farmed salmon. Emerging pathogens, such as infectious salmon anemia virus (ISAV), have generated large economic impacts. Between 2009 and 2011, estimates suggest ISAV reduced salmon production by 700,000 tons, or roughly $2 billion. In addition to this decrease in revenue, additional hidden losses, such as increased production costs, reduced product quality, or altered perceptions of salmon health on the part of the consumer, causes Chile to suffer from lower prices or a loss in market share. Endemic pathogens contribute to approximately 9 to 50% of total mortality counts during a given production cycle. For example, salmonid rickettsial septicemia (SRS) is one of the largest mortality factors during the growth-out production phase of farmed Chilean salmon. In addition, SRS is chiefly responsible for excessive use of antibiotics, generating public concern and market restrictions. However, current strategies to control SRS have not been effective, and key questions, such as its economic impact and assessment of optimal public and private control strategies, have not yet been tackled. The aim of this talk is to highlight the economic impacts of pathogens on the Chilean farmed fish industry. I will also discuss the complex nature of varying incentives that influence producers’ decision-making processes regarding disease control in aquaculture environments.

Bio:  Pablo is a Postdoctoral Scholar at the University of California Agricultural Issues Center, UC Davis since 2017. Before beginning his graduate studies in the US, he worked as a field Veterinarian in the Chilean salmon industry and then in the National Fisheries Service (Sernapesca) to help design the regulatory framework for the salmon production sector. Pablo finished with his Masters in Preventive Veterinary Medicine (MPVM) in 2012, focusing his research on disease management in the Chilean salmon industry. He started his Ph.D. in Epidemiology and Masters in Agricultural and Resource Economics in 2012 and 2013, respectively, with the goal to merge these two fields. His Ph.D. and MS research focused on management of a non-reportable disease, Porcine Reproductive and Respiratory Syndrome (PRRS), in the US swine industry. In addition to this work, Pablo has continued to participate in applied research for the Chilean salmon industry, and between 2014 and 2015 he worked as a research specialist at the University of Minnesota. He completed his Ph.D. and MS degrees in 2017, and was awarded the Agricultural and Resource Economics Department’s Best MS Thesis in the same year.  Pablo has published several articles on disease management in terrestrial and aquatic species, has participated in numerous conferences, delivered invited seminars, and has served as an instructor in workshops within the US and abroad. Pablo’s research focus is on animal health economics and evaluation of public policy.

JEFFREY FISHER, Marine Environment & Food Safety Services

Title of presentation: Fish and Shellfish Disease Management in Ireland

Jeff Fisher, PhD

Director of Marine Environment and Seafood Safety

Marine Institute, Ireland

Abstract: Finfish, molluscan and crustacean disease management in Ireland is guided by EU Directive 2006/88/EC which outlines procedures and protocols for a risk based disease surveillance programme. Irish salmon fisheries consist of a mix of true wild stocks and managed/ranched stocks in addition to commercial salmon production in aquaculture.  As such, the disease challenges for which the Marine Institute is most actively engaged in a diagnostic capacity are problems identified in cultured (and ranched) stocks—the surveillance of the health status of outmigrant wild smolts is not comprehensive across the country (as they fall outside the scope of the legislation).  The disease challenges in the Sacramento basin salmonids can share some similarity in causation, however, in that environmental factors can play a very large role in the manifestation of disease or mortality.  Other factors, such as the introduction of an invasive non-native pathogen can also play a significant role, as the recent isolation of crayfish plague in several freshwater catchments in Ireland reflects.  In this talk, I will profile fish and shellfish disease management in Ireland as it is currently practiced, highlight some of our more pressing challenges at present, and how we are moving forward with further research to inform appropriate management of aquatic animal disease in Ireland and as a Member State of the EU.

Bio:  Dr. Jeff Fisher is the Director of the Marine Environment and Food Safety division of Ireland’s Marine Institute, where he oversees field, laboratory and advisory services and research of a talented group of 80 scientists engaged in fish and shellfish health assessment, environmental chemistry and toxicology, harmful algal bloom and related biotoxin monitoring, reviews of aquaculture licensing applications, and marine spatial planning. Prior to joining the Institute in 2016, he was the Lower Columbia/Washington Coast Branch Chief for the West Coast Region of NOAA-NMFS focused on addressing habitat and water quality factors of decline affecting the recovery of Pacific salmon. Prior to joining NMFS, he worked for a dozen years in environmental consulting where he worked on behalf of both public and private clients on a range of aquatic habitat assessments, restoration design, and aquatic ecological risk assessments. Interspersed with this work he completed a 2-year sabbatical as an American Association for the Advancement of Science Fellow, posted to the US Department of State, Bureau of Oceans and International Environmental and Scientific Affairs, where he managed the invasive species and traditional ecological knowledge portfolios.  He has extensive experience in exposure modeling and analysis of environmental and health risks associated with pesticide and herbicide use, having lead numerous high-profile risk assessments related to the use of such compounds for a variety of programmatic and site specific purposes—including some of significance in California (e.g., Lake Davis northern pike eradication with rotenone, state-wide light brown apple moth eradication treatments). He holds a B.S. in Fisheries from the University of Washington, a M.S. in fish and shellfish pathology from the University of Stirling’s Institute of Aquaculture in Scotland, and a Ph.D. in toxicology from Cornell’s Department of Avian and Aquatic Animal Medicine in the veterinary college.


Title of presentation:  A highly diversified approach to defining the salmon disease-scape in British Columbia and exploring linkages with salmon declines

Dr. Kristi M. Miller-Saunders , BSc, MSc, PhD

Pacific Biological Station

Fisheries and Oceans, Canada

3190 Hammond Bay Rd

Nanaimo, BC Canada V9T 6N7


Abstract: Wild salmon populations have been declining across multiple Pacific salmon species in the Pacific Northwest for 2-3 decades. A Canadian federal judicial inquiry (Cohen Commission) into sockeye salmon declines identified the early marine phase of salmon migration as critical to year class strength, with cumulative and/or synergistic stressors affecting salmon in this vulnerable smolt out-migration stage of prime importance.  Climate and oceanographic-driven variability in the prey- and predator-fields, and infectious disease were determined to be likely drivers of the decline, with the recognition that insufficient data existed on which diseases may cause population-level impacts in the ocean.  Moreover, there was a recognized need for objective scientific advice on the risk of disease transmission posed by the salmon aquaculture industry.  We devised a multidisciplinary program heavily based on genomic technologies to tackle these questions.  The Strategic Salmon Health Initiative program has developed and implemented a number of novel technologies and approaches to elucidate the role of infectious disease in variability salmon survival which has vastly changed our ability to recognize and predict disease and its impact, even in situations where mortality is not observable.  Coupling of high throughput pathogen monitoring, host transcriptome assessments, and novel pathogen discovery through next generation sequencing, with histopathology, in situ hybridization, and tracking and holding studies has begun to reveal the infectious agents with strongest pathogenic potential in sockeye, Chinook and coho salmon, as well as those causing diseases on farms.  This talk will explore the contribution of these approaches to resolve disease phenotypes in BC salmon, and ways in which the program is beginning to translate scientific findings into scientific advice for managers and regulators, and communicate it to the public.

Bio: Dr. Miller obtained her BSc from UC Davis (1984), MSc from University of British Columbia (1986) and PhD from Stanford University (1992), and joined the Pacific Biological Station, Fisheries and Oceans Canada as a Research Scientist two years later.  She is currently the Head of the Molecular Genetics Laboratory at Pacific Biological Station in Nanaimo and an adjunct Professor in the Department of Forest and Conservation Sciences at University of British Columbia.  She is a genetics/genomics subject editor for three journals, Marine and Coastal Fisheries Journal, Immunogenetics and FACETS. 

The Miller laboratory has conducted genetics/genomics research on salmon for 25 years, with applications in fisheries management, conservation, aquaculture, and policy development.   In the past decade, Dr. Miller has led or co-led two multimillion dollar genomics initiatives, “FishManOmics” and the “Strategic Salmon Health Initiative (SSHI)”, both pioneering and applying modern genomic approaches to resolve the stressors and diseases undermining the performance and survival of wild migrating salmon.   Her seminal paper published in Science in 2011 provided the first evidence that infectious disease could be a factor in reduced migratory survival and led to her involvement as a key witness in the “disease” evidentiary hearings at the Cohen Commission of Inquiry.   Current research now focuses most intently on the role of infectious disease in wild salmon declines.   The SSHI project, co-led with Dr. Brian Riddell of the Pacific Salmon Foundation, is providing the most comprehensive assessment of disease impacts on salmon ever undertaken, and the first to integrate intensive pathogen monitoring and physiological profiling of wild, enhancement hatchery and aquaculture salmon.  This project aims not only to ascertain the contribution of infectious disease in declining salmon productivity, but also to provide sound scientific data to inform risk assessments of pathogen transmission between farmed and wild salmon.