Ceratonova shasta is a freshwater, myxozoan parasite that is native to the Pacific North West of North America. It causes enteronecrosis in salmonids which, in the Deschutes River Basin, has resulted in high mortality in cultured juvenile salmon at the Pelton Facility and in adult salmon returning to both the Round Butte and Warm Springs hatcheries. Transmission occurs through waterborne stages: actinospores released from polychaete worms infect salmonid fishes and develop into myxospores which then infect polychaetes (see life cycle on left). The parasite proliferates in each host (not in water). 

“By understanding the relationships between the parasite, its hosts, and the natural habitats and conditions that are favorable or unfavorable for infection, strategies can be developed to limit the exposure of fish to areas where the risk of infection of C. shasta may be higher, or develop management strategies based upon predicted water and climate conditions to improve the survival and viability of wild and hatchery salmonids.” Cyndi Baker, PhD, CTWSRO.

Through collaboration with the Confederated Tribes of the Warm Springs Reservation of Oregon (CTWSRO), USFWS, and ODFW we have developed a parasite monitoring program which contributes to our understanding of the role of pathogens (such as Ceratonova shasta) in juvenile and pre-spawn mortalities of adult Spring Chinook salmon of the Deschutes River Basin. Monitoring is primarily through quantification of waterborne stages of the parasite.


Map of the Deschutes River showing Warm Springs water collection sites
Deschutes River, a tributary of the Columbia River, in central Oregon. Study sites are shown as yellow diamonds. Red circles represent sites at which ISCO water sampling and sentinel fish exposures were conducted. Warm Springs water collection sites in the lower Deschutes River basin.


Water Samples

We conduct two types of water sampling to provide high resolution data on the spatial and temporal abundance of Ceratonova shasta – regular monitoring as well as spatially intensive sporadic longitudinal sampling. Collection of river water samples for regular monitoring occurs at two index sites established in 2015; once a week all year round at Oak Springs and every other week from April through October at Pelton Dam (sites marked in red on map above). Beginning in 2017, monitoring will occur at a further 8 sites that span from the town of Bend to Heritage Landing at the mouth of the Deschutes River (see map on right). Longitudinal sampling occurs approximately twice a year (in spring and summer) at 16-24 sites.

At the established index sites, solar-powered automatic samplers (ISCOs) collect 1L water every 2 hours for 24 hours, from which 4 1L samples are manually taken, whereas samples are collected manually at the remaining index and longitudinal sites. Regardless of collection method, each 1L sample is filtered through a 5-micron nitrocellulose membrane using a vacuum pump, and any captured DNA in 3 of the replicate samples is extracted using a kit. A quantitative PCR (qPCR) specific for C. shasta is used to detect and quantify any parasite DNA present (Hallett & Bartholomew 2006). Cq values generated by the qPCR are converted to numbers of parasite spores per liter of water using reference samples with known quantities of spores. The Warm Springs tribal biologists and members of ODFW are integral to the collection and filtration of the ISCO water samples.


Collecting water samples
on the Deschutes River
Filtering a water sample
using a vacuum pump
Folding the filter paper
with captured material

Longitudinal Water Sampling Schedule

2017:  First on June 6th, second on August 30th
2016:  June 7th, August 30th
2015:  August 17th

Previous Water Sampling Results from Oak Springs

  Previous Water Sampling Results from Pelton Dam



There are multiple genetic types of C. shasta simultaneously present in the Deschutes River Basin (Stinson & Bartholomew 2012). While genotype I infects our target species (Chinook salmon) most commonly, we will be analyzing samples for all genotypes of C. shasta. We do this by amplifying the variable ITS1 region using a qPCR assay and then we sequence that amplicon (Atkinson & Bartholomew 2010). From the sequencing chromatogram, we can determine the proportion of each genotype present in a sample. We use the total spore density to then determine the number of spores of each genotype in a sample.  

Thus, in addition to determining the abundance of total C. shasta in the river, we will also determine the relative proportions of the various genotypes and their spatial and temporal distributions.  These data will be aligned with salmonid migration (juveniles and adults) to investigate whether parasite genotype abundance corresponds with the life history of its salmonid host.



Atkinson and Bartholomew (2010) Disparate infection patterns of Ceratomyxa shasta (Myxozoa) in rainbow trout Oncorhynchus mykiss and Chinook salmon Oncorhynchus tshawytscha correlate with ITS­1 sequence variation in the parasite. International Journal for Parasitology 40:599­604

Hallett SL, Bartholomew JL (2006) Application of a real-time PCR assay to detect and quantify the myxozoan parasite Ceratomyxa shasta in river water samples. Diseases of Aquatic Organisms 71:109-118.

Hallett SL, Ray RA, Hurst CN, et al. (2012) Density of the waterborne parasite Ceratomyxa shasta and its biological effects on salmon. Applied and Environmental Microbiology 78:3724–3731.

Stinson MET and Bartholomew JL (2012) Predicted Redistribution of Ceratomyxa shasta Genotypes with Salmonid Passage in the Deschutes River, Oregon. Journal of Aquatic Animal Health 24:274-280.


These research efforts are possible through contribution (funding and efforts) provided by: CTWSRO, CRITFC-PCSRF (research and graduate support 2017-2018), ODFW (Graduate Fellowship 2015 2016 & 2017-2018), LCRFHC-USFWS

For an overview of Deschutes River studies (sentinel fish exposures and water sampling) conducted in 2015 and 2016, please click on the following link:   “ODFW Fellowship Report 2015-2016”


Image credits: Kalyn Hubbard, Stephen Atkinson.