I undertook a Ph.D. at the University of Queensland, Brisbane, Australia, with Professor Bob Lester and Peter O'Donoghue on "Myxozoan Parasites of Oligochaetes and Fish". I was then awarded an Alexander von Humboldt Research Fellowship to study with Professor Mansour El-Matbouli at the University of Munich, Germany for two years still focusing on myxozoan parasites. Then I procured a post-doc position with Dr Jerri Bartholomew at Oregon State University, USA, in 2003 where I have been studying myxozoan parasites of the Pacific Northwest.
- MB 480 General Parasitology eCampus
- MB 491/591 Diseases of Fish in Aquaculture and Conservation Biology, and the Salmonid Workshop (contributed lectures an labs)
I find parasites fascinating organisms and have always been drawn to the aquatic environment. Thus, I am interested in parasites of marine and freshwater fish. Most of my research has focused on one phylum - the Myxozoa and I've never dissected a fish without encountering at least one of these microscopic, spore-forming, endoparasitic metazoans. Over 2000 are found in fish world-wide and most do not harm their host, but there are several that cause serious diseases (Ceratomyxa shasta, Parvicapsula minibicornis, Myxobolus cerebralis) in the Pacific Northwest of North America. My current research focuses on answering questions about these parasites so that we can make informed management decisions and reduce their impact on native fishes.
- Discovery and description of novel species
- Taxonomy (morphological & molecular characterization)
- Nomenclature (accurate and unambiguous identification and naming of organisms)
- Discovering life cycles
- Molecular diagnoses and development of detection assays
- Enumeration of waterborne stages
- Ecosystem impacts
Disease risks associated with hatcheries in the Willamette River Basin
Funded by: US Army Corp of Engineers; Began: 2011
Personnel: Jerri Bartholomew, Tony Amandi, Rich Holt, Michelle Jakaitis, Sean Roon, Gerri Buckles
The transmission of pathogens between wild and hatchery fishes is not well understood. Wild fish may provide a source of pathogens for hatchery fish and hatchery operations may increase disease risks to wild populations if they serve as point sources that amplify local pathogens. We are combining a range of approaches (sentinel fish exposures, water sampling, wild fish sampling) and lab experiments to gather information on the types and levels of pathogens entering and being released from hatcheries in the Willamette Basin. My major role is to develop water sampling methodologies to directly detect and quantify the following bacterial pathogens: Flavobacterium psychrophilum, F. columnare, Aeromonas salmonisida and Renibacterium salmoninarum; these were selected based on hatchery outbreaks.
Development of a database for pathogens of Oregon fishes
Funded by: Oregon Department of Fish and Wildlife, Sports Fish Restoration; Began: 2011
Personnel: Stephen Atkinson, Casey Dinsmore, Jerri Bartholomew, Tony Amandi, Craig Banner
We are working with The Oregon Department of Fish and Wildlife and OSU’s College of Science IT group (COSINe) to create a comprehensive, searchable, web-based source of information on pathogens of Oregon’s fishes. This database will provide the public (e.g. fishers, hobbyists, students), fish biologists, fish propagation and fish health services staff a reference that will have pertinent information and images of pathogens. The project will create a unique compilation of pathogens of both freshwater and marine fishes, from wild, naturally reared and cultured populations. The database uses a SQL database engine with Drupal webpage interfaces. We plan to go live July 2013.
Clarification of the Pacific North West ‘Manayunkia speciosa’
Personnel: Stephen Atkinson, Julie Alexander, Jerri Bartholomew, Greg Rouse
There is one species of freshwater polychaete in the Pacific North West of North America. It is host to several parasites, including two myxozoans, Ceratomyxa shasta and Parvicapsula minibicornis. Investigations into the genetic diversity of the worm revealed that it differs to the type described from the Great Lakes, and elsewhere. This has prompted assignment of the PNW species to a new species and a comprehensive morphological characterization, including light and scanning electron microscopy.
Investigations into Myxozoans in Waterfowl
Funded by OSU General Research Fund, Dept. Microbiology Tartar Award
Personnel: Stephen Atkinson, Jerri Bartholomew
A nation-wide collaboration resulted in the description of the first myxozoan known from birds, Myxidium anatidum. This discovery questions whether we have witnessed the recent emergence of a novel parasite or a host-switching event (e.g. from fish to aquatic bird). Dr. Bartholomew and I have a grant from the OSU General Research Fund to further explore this intriguing relationship and to determine if all six documented US cases were caused by one or more species of myxozoans and to determine the infectious cycle. This will involve molecular methods and a field trip to Georgia, USA.
Ph.D. at the University of Queensland, Brisbane, Australia
Book chaptersBartholomew, J.L., Atkinson, S.D., Hallett, S.L., and Alexander, J.D. 2021. Myxobolus cerebralis; in Fish Parasites: A handbook of protocols for their isolation, culture, and transmission Eds Sitjà-Bobadilla, A., Bron, J.E., Wiegertjes, G., Piazzon, M.C.; 5M Books, Sheffield, UK.
- Bartholomew, J.L., Atkinson, S.D., Hallett, S.L., and Alexander, J.D. 2021. Ceratonova shasta; in Fish Parasites: A handbook of protocols for their isolation, culture and transmission Eds Sitjà-Bobadilla, A., Bron, J.E., Wiegertjes, G., Piazzon, M.C.; 5M Books, Sheffield, UK.
- Hallett, S.L., Hartigan, A., and Atkinson, S.D. 2015. Myxozoans on the move: dispersal modes, exotic species and emerging diseases. In: Myxozoan Evolution, Ecology and Development Okamura B, Gruhl A, Bartholomew JL (eds). Springer.
- Hallett, S.L., Atkinson, S.D., Bartholomew, J.L. and Székely, C.S. 2015. Myxozoans exploiting homeotherms. In: Myxozoan Evolution, Ecology and Development Okamura B, Gruhl A, Bartholomew JL (eds). Springer.
- Fontes, I., Hallett, S.L., and Mo, T.A. 2015. Comparative epidemiology of myxozoan diseases. In: Myxozoan Evolution, Ecology and Development Okamura B, Gruhl A, Bartholomew JL (eds). Springer.
- Alexander, J.D., Kerans, B.L., El-Matbouli, M., Hallett, S.L., and Stevens, S.L. 2015. Annelid-myxosporean interactions. In: Myxozoan evolution, Ecology and Development Okamura B, Gruhl A, Bartholomew JL (eds). Springer.
- Bartholomew J.L. and Hallett S.L. 2013. Myxobolus cerebralis. In: Invasive Species Compendium. CABI, Oxfordshire, UK. http://www.cabi.org/isc/datasheet/73782
- Hallett S.L. and Bartholomew J.L. 2012. Chapter 8: Myxobolus cerebralis and Ceratomyxa shasta. In: Fish Parasites: Pathobiology and Protection. Editors: Woo P.T.K. & Buchmann K. CABI, Oxfordshire, UK.
Journal articlesBorzák, R., Borkhanuddin, M.H., Cech, G., Molnár, K., Hallett, S.L., and Székely, C. 2021. New data on Thelohanellus nikolskii Achmerov, 1955 (Myxosporea, Myxobolidae) a parasite of the common carp (Cyprinus carpio, L.): the actinospore stage, intrapiscine tissue preference and molecular sequence. Intl. J. for Parasitol. Parasites and Wildlife 15: 112-119.
- Lehman, B.M., Johnson, R.C., Adkison, M., Burgess, O.T., Connon, R.E., Fangue, N.A., Foott, J.S., Hallett, S.L., Martinez–López, B., Miller, K.M., Purcell, M.K., Som, N.A., Valdes–Donoso, P., and Collins A.L. 2020. Disease in Central Valley Salmon: Status and Lessons from Other Systems. San Francisco Estuary and Watershed Sci. 18 (3) Article 2: 1-31. https://doi.org/10.15447//sfews.2020v18iss3art2.
- Robinson, H.E., Alexander, J.D., Hallett, S.L., and Som, N.A. 2020. Management Brief: Prevalence of infection in hatchery‐origin Chinook Salmon correlates with abundance of Ceratonova shasta spores: implications for management and disease risk. North American J. of Fish. Mgmt. 40: 959-972.
- Richey, C.A., Kenelty, K.V., Van Stone Hopkins, K. Stevens, B.N., Martinez-Lopez, B., Barnum, S.M., Stevens, B.N., Hallett, S.L., Atkinson, S.D., Bartholomew, J.L., and Soto, E. 2020. Validation of environmental DNA sampling for determination of Ceratonova shasta (Cnidaria: Myxozoa) distribution in Plumas National Forest, CA. Parasit. Res. https://doi.org/10.1007/s00436-019-06509-1.
- Howell, C.K., Atkinson, S.D., Bartholomew, J.L., and Hallett, S.L. 2019. Development and application of a qPCR assay targeting Ichthyophthirius multifiliis in environmental water samples. Dis. of Aquatic Org. 134:43-55.
- Atkinson, S.D., Hallett, S.L., Diaz Morales, D., Bartholomew, J.L. and deBuron, I. 2019. First myxozoan infection (Cnidaria: Myxosporea) in a marine polychaete from North America and erection of actinospore collective group Saccimyxon. J. of Parasit. 105:252-262.
- Javaheri, A., Babbar-Sebens, M., Miller, R.N., Hallett, S.L., and Bartholomew, J.L. 2019. An adaptive ensemble Kalman filter for assimilation of multi-sensor, multi-modal water temperature observations into hydrodynamic model of shallow rivers. J. of Hydrology 572:682-691.
- Javaheri, A., Babbar-Sebens, M., Alexander, J.A., Bartholomew, J.L., and Hallett, S.L. 2018. Global sensitivity analysis of water age and temperature for informing salmonid disease management. J. of Hydrology 561:89-97.
- Atkinson, S.D., Hallett, S.L., and Bartholomew, J.L. 2018. Genotyping of individual Ceratonova shasta (Cnidaria: Myxosporea) myxospores reveals intra-parasite ITS-1 variation and invalidates the distinction of genotypes II and III. Parasit. 145:1588-1593.
- Richey, C.A., Kenelty, K.V., Van Stone Hopkins, K., Stevens, B.N., Martinez-Lopez, B., Barnum, S.M., Hallett, S.L., Atkinson, S.D., Bartholomew, J.L., and Soto, E. 2018. Distribution and prevalence of Myxobolus cerebralis in postfire areas of Plumas National Forest: Utility of environmental DNA sampling. J. of Aquatic Animal Hlth. 30:130-143.
- de Buton, I., Hill-Spanik, K.M., Haselden, L., Atkinson, S.D., Hallett, S.L., and Arnott, S.A. 2017. Infection dynamics of Kudoa inornata (Cnidaria: Myxosporea) in spotted seatrout, Cynoscion nebulosus (Teleost: Sciaenidae). Dis. of Aquat. Org. 127:29-40.
- Chiaramonte L.V., R. A. Ray, R. Alex Corum, Toz Soto, S.L. Hallett and Bartholomew, J.L. 2016. Klamath River Thermal Refuge Provides Juvenile Salmon Reduced Exposure to the Parasite Ceratonova shasta. Transactions of the American Fisheries Society 145: 810-820.
- Foott J.S., Stone R., Fogerty R., True K., Bolick A., Bartholomew J.L., Hallett S.L., Buckles G.R., and Alexander J.D. 2016. Production of Ceratonova shasta myxospores from salmon carcasses: Carcass removal is not a viable management option. Journal of Aquatic Animal Health 28: 75-84.
- Hurst C.N., Wong P., Hallett S.L., Ray R.A., and Bartholomew J.L. 2014. Transmission and persistence of Ceratonova shasta genotypes in Chinook salmon. Journal of Parasitology 100: 773-777.
- Alexander, J.A., Hallett, S.L., Stocking, R. W., Xue, L. and Bartholomew, J.L. 2014. Host and parasite populations after a ten year flood: Manayunkia speciosa and Ceratonova (syn Ceratomyxa) shasta in the Klamath River. Northwest Science 88: 219-233.
- Hallett, S.L., Ray, R.A., Hurst, C.N., Holt, R.A., Buckles, G.R., Atkinson, S.D. and Bartholomew, J.L. 2012. Density of the Waterborne Parasite, Ceratomyxa shasta, and Its Biological Effects on Salmon. Applied and Environmental Microbiology 78: 3724-3731.
- Zielinski C.M., Lorz H.V., Hallett S.L., Xue L. and Bartholomew J.L. 2011. Comparative susceptibility of Deschutes River (Oregon, USA) Tubifex tubifex populations to Myxobolus cerebralis. Journal of Aquatic Animal Health 23: 1-8.
- Hallett, S.L. and Bartholomew, J.L. 2009. Development and application of a duplex QPCR for river water samples to monitor the myxozoan parasite Parvicapsula minibicornis. Diseases of Aquatic Organisms 86: 39-50.
- Hallett S.L., Lorz H.V., Atkinson S.D., Rasmussen C., Xue L. and Bartholomew J.L. 2009. Propagation of the myxozoan parasite Myxobolus cerebralis by different geographic and genetic populations of Tubifex tubifex: An Oregon perspective. Journal of Invertebrate Pathology 102:57-68.
- Székely Cs., Hallett S.L., Atkinson S.D. and Molnár K. 2009. Complete life cycle of Myxobolus rotundus Nemeczek, 1911 (Myxosporea: Myxobolidae), a gill myxozoan of the common bream (Abramis brama). Diseases of Aquatic Organisms 85: 147-155.
- Molnár K., Székely Cs., Hallett S.L. and Atkinson S.D. 2009. Some remarks on the occurrence, host specificity and validity of Myxobolus rotundus Nemeczek, 1911 (Myxozoa: Myxosporea). Systematic Parasitology 72: 71-79. DOI 10.1007/s11230-008-9161-7.
- Hallett, S.L. and Bartholomew, J.L. 2008. Effects of water flow on the infection dynamics of Myxobolus cerebralis. Parasitology 135: 371-384 doi: 10.1017/S0031182007003976.
- Bartholomew J.L., Atkinson S.D., Hallett S.L., Lowenstine L.J., Garner M.M., Gardiner C.H., Rideout B.A., Keel M.K., and Brown J.D. 2008. Myxozoan parasitism in waterfowl. International Journal for Parasitology 38: 1199-1207.
- Garner M.M., Atkinson S.D., Hallett S.L., Bartholomew J.L., Nordhausen R.W., Reed H., Adams L. and Whitaker B. 2008. Renal myxozoanosis in weedy sea dragons, Phyllopteryx taeniolatus (Lacepède), caused by Sinuolinea phyllopteryxa n. sp. Journal of Fish Diseases 31: 27-35.
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