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Spironucleosis salmonicida

Overview​

What is Spironucleosis salmonicida?​

Spironucleosis is a disease caused by the single celled parasite Spironucleus salmonicida affecting farmed Atlantic salmon, Arctic charr, and Chinook salmon and lumpfish 6. It was first known in 1989, from aquaculture farms in northern Norway, Finnmark and soon after in British Columbia. Outbreaks have since occurred sporadically in Northern Norway, sometimes with decade-long intervals; most recent and largest outbreak was 2022–2023 1. Outbreaks have been linked to a single smolt facility and then traced back to lakes, believed to be the natural reservoir with brown trout and Arctic Charr 5

At a glance​

  • Where: Outbreaks so far only in northern Norway (mostly Finnmark, plus one char farm in Vesterålen) 5, 7, 11.
  • How often: Rare. Outbreaks have come roughly every ten years: 1989–91, 2001, 2007–08 and 2022–23 6, 11.
  • How it gets in: Almost all salmon outbreaks trace back to one smolt facility. Wild trout and char in its water source carry the parasite, and infected smolt are then moved to sea 5.
  • How it spreads at sea: From cage to cage on the same site. Spread between sites through the water has not been shown and is judged very unlikely 5.
  • How fast: Slowly in salmon. Infected fish can look healthy for weeks. In trials, lesions took 6–8 weeks to appear, with any deaths after that 5 , 6. Some fish die suddenly with no signs 5
  • Mortality: Can be sudden and high if pathogen goes to the brain, or can develop more slowly over weeks 11. Muscle abscesses add large losses through culling, discards and downgrading; in an early outbreak up to 60% of harvested fish were discarded 8.
  • Treatment: None available 5, 1, 11.

Clinical Signs of Spironucleosis​

Common Signs​

  • Physical Signs:

    • Pus filled cavities in the muscles: often present at tail and under skin 5
    • Exophthalmia: Bulging of one or both eyes, potentially accompanied by fluid accumulation or abscess formation behind the eyes 5
    • Tail swelling: Swelling or bulging at the base of the tail fin, which may later extend to the dorsal fin. Caused by blood or pus-filled cavities in the musculature, sometimes visible through the skin as yellowish areas 5
    • Fluid filled swim bladder: May also have thickened walls 5
    • Light spots on kidney and liver: Areas of tissue death and often soft 5
    • Heart: Grayish veil from an inflamed epicardium and the pericardial cavity may contain large numbers of flagellates (microscope needed) 5
    • Bloody fluid around the brain: Potentially the cause of some acute mortality cases 5
    • Note on Host Species: In Arctic charr and Chinook salmon, symptoms differ from Atlantic salmon: no granulomas in muscle/organs, but vast aggregates of parasites in the vasculature of most organs 4. Lumpfish show few signs. Some have exophthalmia and pale gills. Dead fish have pale hearts, watery blood and liver damage, and they die suddenly while still feeding 6

  • Behavourial Changes:

    • Abnormal swimming, and loss of balance in some fish 5

  • Progression of Symptoms

    • The disease has three broad phases — a transient gut phase, a blood phase where flagellates circulate freely, and a chronic tissue phase where surviving parasites hole up in boils/abscesses in muscle, skin, liver, kidney, behind the eyes, or around the heart and brain 5.
    • Severity of the symptoms and progression depend on the host species and the strain of the S. salmonicida 5. Individual immunity may also exist, as some Atlantic salmon have remained uninfected following injection 6
    • Acute and Chronic infection:
      • Acute course: fish may die suddenly with no external signs, likely from parasites invading the brain causing haemorrhage 5
      • Chronic course: Fish remain in apparently good condition but may be stunted or thin, show abnormal behaviour like balance problems. Mortality then increases and the above described signs can be seen 5
    • In the Population:
      • Infected fish can look healthy. In a lab challenge, 78% of salmon had the parasite in the blood after three weeks, yet none were sick 6.
      • The parasite is cleared in some fish. Antibodies appear after about 6–9 weeks and the blood load falls 5, 7. In others it survives in abscesses, which can still be present at slaughter after the outbreak is over 511.
      • In a 17-week trial, fewer than a quarter of the salmon developed lesions 7.
      • On a site with an outbreak, infection pressure builds up and more cages are affected over time 5.

Causes of Spironucleosis​

Etiology

Causative agent: Spironucleus salmonicida (diplomonad anaerobic flagellate)

  • Occurs naturally in the gut of apparently healthy wild brown trout and Arctic char in lakes in Troms and Finnmark 5, 3
  • There are 3 species of Spironucleus that occur in the gut of salmonids, but only S. salmonicida is considered pathogenic, causing a systemic (spread throughout the body) infection 5. Spironucleus barkhanus and Spironucleus salmonis are both considered harmless gut commensals; S. salmonis is additionally known to form cysts as part of its life cycle 5
  • Formerly classified as S. barkhanus; redescribed as a distinct species in 2006
  • Considered the “salmon killer” due to high mortality risk once established 1
  • Despite a strictly anaerobic metabolism and lack of normal eukaryotic antioxidant systems, it survives in oxygen-rich host tissues. It appears that the parasite uses oxygen as a trigger to know it is getting towards the more oxygen rich outer wall of the gut, and then out into the blood 2
  • Other Spironucleus species cause systemic disease in other fish (non salmonid) species — e.g. S. anguillae in eels in Poland, S. vortens in aquarium angelfish 5

Transmission Methods The exact transmission path is unknown. The best guess is wild trout and char, then intake water, then smolt 511.

  • Contaminated intake water at smolt facilities (probable route). Wild brown trout and Arctic char in the water source carry S. salmonicida. If UV disinfection is missing or too weak, the parasite may reach the smolt. This route has not been proven 5, 11
  • S. salmonicida may survive outside fish longer than lab tests suggest. In clean fresh water it lives only about 10 minutes at most 5. But it carries genes for building cyst walls, and a tough cyst stage could last much longer. No cysts have been found yet 11. Leftover nutrients lengthened its survival in brackish water 5, and a related species lives longer in faeces than in clean water 5. Neither has been shown for S. salmonicida in fresh water.
  • Cage-to-cage transmission after sea transfer — infected carriers shed the parasite via pus, mucus, blood, and possibly feces, infecting pen-mates 5
  • Wound/skin colonization — flagellates can colonize minor wounds and skin lesions, a plausible entry route given how common small wounds are in farmed fish 5
  • Sea lice as a possible mechanical vector — theoretical route between salmon, and possibly salmon-to-lumpfish 5
  • Contaminated processing wastewater — implicated in one historical outbreak near a slaughterhouse outflow 5
  • Farm-to-farm spread via open water — not demonstrated, considered very unlikely under current site-distance regulations 5

Other Fish Hosts

  • Artic Charr: Salvelinus alpinus is both a natural wild host and one of only four species known to carry S. salmonicida in sea farms, alongside salmon, farmed Chinook, and lumpfish. Farmed sea charr can develop systemic infections — abnormal swimming, bulging eyes, and heavy numbers of flagellates in the blood and organs — but mortality tends to be low, and in challenge experiments charr proved only mildly susceptible compared to salmon and lumpfish 5

  • Trout:

    • Rainbow trout. Do not appear to be susceptible 3. In injection trials with a Norwegian isolate, only Atlantic salmon were infected. Blood plasma from rainbow trout, chinook and coho killed the parasite in test tubes, which suggests innate immunity 5.
    • Brown trout. Resistant to disease but able to carry the parasite. Wild freshwater trout carry it in the gut without being ill 5. In a sea trout trial, infections were mild and short-lived, with no lesions, but infected trout and salmon passed the parasite on to each other 7.

  • Lumpfish:

    • Lumpfish were found infected in pens where the salmon had spironucleosis 5
    • Lumpfish can be more susceptible than salmon and mortality can happen quickly (i.e there is still faeces in intestine, showing they were eating) with large amounts of flagellates in the system 6.
    • Where signs did appear: varying degrees of exophthalmia (sometimes one eye, sometimes both, occasionally severe), pale gills in some sick fish 6
    • At necropsy of dying/dead fish: pale hearts, watery blood, necrotic foci on the liver, and large numbers of flagellates in blood, peritoneal fluid, stomach and intestine 6

  • Chinook salmon:

    • Involved in the original 1991 outbreak in British Columbia that helped identify S. salmonicida. It is highly susceptible and develops strong infections to the BC strain, but is fairly unaffected by the Norwegian strain 5
    • One study using the BC isolate found the parasite dies quickly in freshwater and full seawater, surviving longest in brackish water 10

Risk Factors

  • RAS and smolt facilities. Long water retention, high nutrient levels and dense stocking let pathogens build up in RAS water and biofilm 1. How S. salmonicida behaves in RAS is poorly known.
    • In a 2026 trial it did not establish in the biofilter or on tank walls, with or without UV or ozone, so it is unclear whether loop disinfection protects 1.
    • The disease has so far been seen only at sea, but the parasite is probably more widespread than known, so it could occur in hatcheries, especially as fish spend longer on land 11.
    • Freshwater infection experiments produced abscesses and high mortality in salmon 6.
  • Lakes as water sources. Wild brown trout and Arctic char in source lakes are the known reservoir 5. Test source water when building or extending a smolt facility with salmonids in its water source 11. Salmon lice, particularly Caligus elongatus, might carry the parasite from fish to fish. This is possible but not shown 5.
  • Temperature. It does not survive much above 15 °C. Outbreaks happened at 6–10 °C. It is unlikely to persist in southern Norwegian farming 5, 11
  • Intensive farming. Dense stocking and husbandry stress may make transmission easier 1,4. Experimental transmission ranged from very low to high, so this is a suspected risk, not a proven one 5, 6, 7.

Diagnosis​

Diagnostic Methods

  • Light Microscope with a fresh smear: Put abscess contents, blood or body fluid under the microscope at 100–400x. Look for swarms of fast-moving, pear-shaped flagellates with six front and two rear tails 5, 7. This can be used to identify the genus, but with 2 other species also present in the gut of salmon, or even in cysts ( S. salmonis), DNA analysis is needed 11. A scanning electron microscopy for detailed morphology (8 flagella: 6 anterior, 2 posterior)1

  • Gross pathology: at slaughter/necropsy, looking for: Pale soft spots (necrosis) on liver, kidney, occasionally spleen; opaque fluid or boils behind the eyes (especially with exophthalmia); greyish film on the heart (epicarditis), pericardial cavity may contain large numbers of flagellates; fluid-filled swim bladder with thickened wall; pus-filled cavities (boils) in the musculature, most commonly at the tail/caudal fin base, then dorsal fin base — sometimes invisible until filleting. Boil contents are often blood-tinged 5

  • PCR and qPCR: Confirm by PCR. Both conventional PCR and qPCR are available at the Norwegian Veterinary Institute 5, 11

    • Targeting the 18S rRNA region of S. salmonicida (TaqMan assay; Miller et al. protocol); threshold CT value of 35.
    • RT-qPCR detection rates differed substantially between blood and gut swab samples, and post-mortem detection is best from head kidney in salmon but foregut/gills in Arctic char — gut samples taken behind the last caecum appear poorly suited for detecting infection 6

  • Culture viability: Parasite cultured in Keister’s Complete Medium at 12°C under anaerobic conditions 1

  • Timing matters. Blood is positive in the first weeks. As antibodies build, the parasite leaves the blood and hides in lesions 5, 7.

  • Sample several tissues, including gut 11. In trials, kidney and tail muscle worked best for carrier fish 5,6.

Differential Diagnosis Intestinal damage can be confused with coccidiosis or Infectious Pancreatic Necrosis (IPN), especially if there is overgrowth of S. salmonis in the gut 5.

Treatment and Prevention​

  • No approved treatment exists 5, 1,11
    • Nifurazolidone showed no clear effect in Norwegian farmed salmon or chinook 5
    • Metronidazole works and can be used for ornamental fish, but not food fish, it has been banned in Europe since the late 1990s because it can cause cancer 1.
  • Biosecurity and prevention are the only currently viable management strategies 1, 5

Prevention

  • Treat intake water with UV. Primary measure and best tested option. Medium-pressure (MP) lamps at 50 mJ/cm² or more killed all parasites in the lab 5, 1.
    • The old standard of 25 mJ/cm² is not enough 5, 1.
    • Cloudy water or high organic load can reduce UV effect, so higher doses may be needed 5, 1
  • When building or extending a facility with salmonids in the water source, test the source for S. salmonicida 11
  • Lumpfish should not be used as cleaner fish in salmon cages that are prone to S. salmonicida infections 6

Case Studies​

Real-World Examples

Norway

  • 1989: First case of systemic spironucleosis (then called hexamitosis) in farmed Atlantic salmon, reported from a marine fish farm in northern Norway. More cases during early 1990s.
  • 2001 case in Finmark, then 2002 it was detected in farmed trout in Vesterålen, Northern Norway. 2008 there were also a case, which was traced back to a smolt provider 9
  • Northern Norway (2022): Finnmark, 2022. The largest outbreak so far. Around a dozen grow-out sites were affected, most stocked from the same smolt facility. Losses came from deaths, culling and downgrading, and the last fish were harvested in 2024. One producer's losses were estimated at up to NOK 900 million 6, 7 Lumpfish on affected sites were also found infected 6 ,1, 8

British Columbia, Canada

  • 1991 — seawater pen-reared Chinook salmon near Sechelt, BC. This is the original case that led to identification of what's now called S. salmonicida (initially described as an unusual Hexamita-like flagellate) 10. Also found in wild Arctic char in Nunavut 5.

Response Strategies:

  • 2008 there was an investigation tracing back to a lake with brown trout and charr that had the flagellates in their guts 9
  • This 2022, Northern Norway outbreak resulted in the instigation of SpiroFri project — Link to Study which lead it to be traced to one smolt factility. The water source is thought to be source 5

Economic Impact​

  • Fillet quality losses: Boils in the fillet have historically led to discard rates of up to 60% in slaughter fish — a major source of economic loss separate from mortality itself. All fish must be individually checked at filleting 5
  • Grieg Seafood revealed that the S. salmonicida parasite had cost the company some $90 million in downgraded fish since 2022 8
  • Outbreak costs: The 2022–2023 outbreak in Finnmark, northern Norway, caused high mortality, major economic losses, and reduced fish welfare,6 with total costs estimated at around NOK 1 billion 5

Research and References​

Latest Research Findings​

  1. "Interplay between disinfection and the enigmatic diplomonad parasite Spironucleus salmonicida in Atlantic salmon" Authors: Carlo C. Lazado, Hanne Brenne, Didrik Olaisen, Gunhild S. Johansson, Miroslava Hansen, Bjørn-Steinar Saether, Jelena Kolarevic, Gerrit Timmerhaus, Torstein Tengs & Lill-Heidi Johansen Main Finding: "Overall, S. salmonicida was sensitive to medium-pressure UV, and under the tested conditions did not persist or cause disease in RAS." Link to study
  2. "Spironucleus salmonicida infections and spironucleus in Norwegian aquaculture: Transmission routes, host spectrum and prevention (SpiroFri)" Project Leader: Egil Karlsbakk Main Findings:
    • Lumpfish (rognkjeks) can develop serious disease upon infection with S. salmonicida, making them unsuitable for facilities experiencing spironucleosis outbreaks 6.
    • Brown trout and Charr can infect salmon, even if they are not sick themselves. Links to Study

Conclusion​

Systemic spironucleosis, caused by Spironucleus salmonicida, is a rare but costly threat to salmon farming in northern Norway. Salmon outbreaks occurred in 1989–91, 2001, 2007–08 and, most severely, 2022–23. Almost all traced back to a single smolt facility. Infected fish can look healthy for weeks, and abscesses in the muscle cause losses at slaughter as well as deaths. No treatment is available or permitted for food fish, so prevention is the only practical control. The best-supported measure is to disinfect intake water at smolt facilities with medium-pressure UV at 50 mJ/cm² or more, although the exact route of infection is still unproven.

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Last Modified
30-10-2026

Last Reviewed

Citations

[1] Lazado, C.C., Brenne, H., Olaisen, D. Interplay between disinfection and the enigmatic diplomonad parasite Spironucleus salmonicida in Atlantic salmon. Sci Rep (2026). https://doi.org/10.1038/s41598-026-51626-4. https://www.nature.com/articles/s41598-026-51626-4

[2] Stairs CW, Kokla A, Ástvaldsson Á, Jerlström-Hultqvist J, Svärd S, Ettema TJG. Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida. BMC Biology. 2019;17:19. https://doi.org/10.1186/s12915-019-0634-8. https://link.springer.com/article/10.1186/s12915-019-0634-8

[3] Jørgensen, A., Torp, K., Bjørland, M., & Poppe, T. (2011). Wild Arctic char Salvelinus alpinus and trout Salmo trutta: hosts and reservoir of the salmonid pathogen Spironucleus salmonicida (Diplomonadida; Hexamitidae). Diseases of Aquatic Organisms, 97(1), 57–63. https://doi.org/10.3354/dao02404

[4] Williams CF, Lloyd D, Poynton SL , Jorgensen A, Millet COM, et al. (2011) Spironucleus species: Economically-Important Fish Pathogens and Enigmatic Single-Celled Eukaryotes. J Aquac Res Development S2:002. doi:10.4172/2155-9546.S2-002 https://www.researchgate.net/profile/Catrin-Williams-8/publication/269540397_Spironucleus_species_Economically-Important_Fish_Pathogens_and_Enigmatic_Single-Celled_Eukaryotes/links/57cf28e008ae83b3746235a3/Spironucleus-species-Economically-Important-Fish-Pathogens-and-Enigmatic-Single-Celled-Eukaryotes.pdf

[5] Karlsbakk E, Tjessem A, Hansen H, Sterud E (2025) Spironucleus-infeksjoner og Spironucleose hos laks – # Spironucleus infections and Spironucleosis in salmon – A knowledge summary 2025-59. Havforskningsinstituttet (Institute of Marine Research, Norway). ISSN 1893-4536. Published 28.10.2025. https://www.hi.no/hi/nettrapporter/rapport-fra-havforskningen-2025-59

[6] Kvamme BO, Sandlund N, Mæhle S, Berg-Rolness H, Austgulen MH, Sengee A, Ghebretnsae DB, Nordbø J, Skår C, Lofnes A, Karlsbakk E (2025) Smitteforsøk med Spironucleus salmonicida på rognkjeks og laks. Rapport fra havforskningen 2025-65. Havforskningsinstituttet. ISSN 1893-4536. Published 28.10.2025. Link: https://www.hi.no/hi/nettrapporter/rapport-fra-havforskningen-2025-65

[7] Karlsbakk, E., Austgulen, M. H., Nordbø, J., Aga, J. M., Berg-Rolness, H., Mæhle, S., ... & Kvamme, B. O. (2025). Is sea trout susceptible to Spironucleus salmonicida-the parasite that can cause systemic spironucleosis in farmed Atlantic salmon? Infection trials on sea trout and Atlantic salmon. Havforskningsinstituttet (Institute of Marine Research, Norway). https://www.hi.no/hi/nettrapporter/rapport-fra-havforskningen-2025-82

[8] News article: "Spironucleus salmonicida: Inside the ‘salmon killer’ parasite" (Feb 27, 2024) Salmon Business. https://www.salmonbusiness.com/spironucleus-salmonicida-inside-the-salmon-killer-parasite/

[9] Johansen, R., Kongtorp, R.T., Bornø, G., et al. (2009_Fiskehelserapporten 2008_. Veterinærinstituttet (Norwegian Veterinary Institute annual fish health report) (https://www.vetinst.no/rapporter-og-publikasjoner/rapporter/2009/fish-health-report-2008)

[10] Kent, M. L., Ellis, J., Fournie, J. W., Dawe, S. C., Bagshaw, J. W., & Whitaker, D. J. (1992). Systemic hexamitid (Protozoa: Diplomonadida) infection in seawater pen-reated chinook salmon Oncorhynchus tshawytscha. https://www.cabidigitallibrary.org/doi/full/10.5555/19950800356

[11] Haakon Hansen. Norwegian Veterinary Institute. "Spironucleosis" . Updated 15th Dec, 2025 https://www.vetinst.no/sykdom-og-agens/spironukleose Accessed Sept, 2026