Understanding E. cuniculi
E. cuniculi (Encephalitozoon cuniculi or EC) is an obligate intracellular (that can only reproduce inside the host's cells) microscopic parasitic protozoan (but later classified as a fungus) that belongs to the phylum Microsporidia (pore-forming unicellular parasites).
This parasite causes encephalitozoonosis which can affect rodents, horses, rabbits, carnivores as well as immunocompromised human beings such as HIV/Aids and Cancer patients. The EC is often noted in rabbits making them be accepted as their principal hosts  and it commonly affects laboratory and house rabbits with a 52% prevalence . However, it is rare in wild rabbits.
Encephalitozoon cuniculi parasite can find its way into various internal organs including the brain, spinal cord, kidney, lungs, liver, and be inactive for a long time.
However, when the affected animal's immunity becomes weak due to diseases, stress, etc., this parasite can begin to reproduce causing organ and nervous system inflammation (due to this parasite's effect or reaction of the immunity system) as well as the rapture of the cells among other clinical signs.
The EC is predominant in dwarf breeds. Also, it causes eye disease in younger rabbits and for the middle age to older ones, it causes nervous system diseases. This parasite has been noted in African, American, Europe, and Australia.
Encephalitozoon cuniculi transmission
The common ways through which the Encephalitozoon cuniculi is transmitted include the following:
1. Through urine and feces
Being a spore-producing parasite, rabbits eliminate spores it produces from their bodies through feces and urine. Therefore, ingestion of food (such as hay, grass, greens), water that has these infective spores (able to cause infections) is one way how this protozoan is transmitted.
Once ingested, the spores infect the intestinal absorptive cells before spreading to the brain, kidney, liver, other organs.
In the kidney, the E. cuniculi reproduce, and some of this parasite's spores are passed through the urine after about 6 weeks. Usually, “spores in the urine peak 2 months post-infection and end 3 months post-infection”.
The other way is the inhalation of the microsporidian spores. Once inhaled, they can find a way to the various organs they affect through the lungs.
3. Vertically through the placenta
Pregnant rabbits can transmit EC through their placenta if they are infected while pregnant and it often goes to the lens of the kit's eye causing rapture, cataract and possibly serious eye diseases including uveitis.
The EC infection shows symptoms in only a small percentage of affected animals especially those stressed, under poor nutrition, or have weakened immunity.
In pet rabbits, E. cuniculi can show the following symptoms.
- Head tilt (torticollis), neck spasm, seizures, urinary incontinence, hind leg weakness, partial paralysis (paresis), uncoordinated movement (ataxia), circling, rolling, and other neurological diseases
- Kidney disease – It destroys kidney cells. This might result in increased urination, thirst, weight loss and kidney failure (renal failure).
- Eye disease – cloudy eyes and cataract
- Blindness and cataract in kits
- Brain inflammatory lesions which may cause subtle difficulties in chewing, inhaling while eating and urine control.
- Eye lens rapture characterized by excessive tearing, redness, swelling, and inflammation
- Some generalized symptoms may include anorexia, lethargy, weight loss, rapid breathing after exercise or reluctance to exercise in case of heart damage.
Not that head tilt in rabbits could also be due to spinal trauma, splay leg, listeria infection, infection in the middle ear, lead toxicity as well as Toxoplasma. 
Diagnosis is by a blood test or serology in rabbits showing clinical signs such as eye inflammation, kidney disease, or neurological ones. Some of the blood tests may include ELISA titer to measure EC antibody levels and protein electrophoresis.
Since some symptoms may resemble Toxoplasma gondii, Pasteurella multocida, Baylisascaris procyonis, or Listeria monocytogenes, the differential diagnosis may be recommended. 
There are two antibodies tested, the IgM and IgG and the former indicated EC infection
Note that collecting blood samples so early or if your rabbit has a weak immunity that it does not produce antibodies may not reveal the presence of EC . Take a sample a few weeks later.
However, diagnosis is elusive and expensive since research shows that over 50% of healthy laboratory and domestic rabbits have the EC antibodies.
Taking two blood samples at different times may help indicate if EC is flaring up (an indication that there is a present infection) or if it is reducing, that will may indicate recovery from encephalitozoonosis.
Also, a PCR urine swab can help identify the presence of the EC DNA in the urine. This will confirm that your pet has this parasite and it is shedding. However, a negative test does not indicate absence but could also indicate it is no shedding.
Finally, a CT scan or MRI may be used in case of a suspected brain lesion if your rabbit has neurological issues.
Treatment and E. cuniculi recovery
Treatment therapy and response will depend on the severity of the infection. Treatment will involve antiparasitic medications such as fenbendazole (Panacur® or Lapizole®) at 20 mg/kg for up to 4 weeks as well as supportive and nutritional care. 
Also “benzimidazole medications such as albendazole and oxibendazole” have been used but there is no universally agreed protocol for treating encephalitozoonosis.
All these treatments can cause anemia, leukopenia and thrombocytopenia – low red blood cells, white blood cells, and platelets count respectively.
If your rabbits do not eat, they may develop GI complications including GI stasis. Offer moisty fresh leafy greens as well as syringe feeding with Emeraid Herbivore or Oxbow Critical Care for Herbivores.
You may also require medications to deal with various symptoms such as dizziness ( with medicines like Meclizine) and head tilt, inflammation eye drops and support for those that have hindleg paralysis and ataxia. Corticosteroids can be used as an anti-inflammatory if there is a proper renal function.
Uncontrollable seizures if no encephalitozoonosis treatment or failure to respond to treatment may be expected as well as cataract development and blindness.
There isn't enough evidence that the treatments will cure the disease and euthanasia may be recommended in case of severe symptoms.
Finally, prognosis is guarded depending on the response to treatment, severity and the effect that the parasite may have already caused. Morbidity in young rabbits is about 15%.
Whereas the parasite can survive inside hutches or rabbit housing for months especially if they are cool and humid and at least a month in dry conditions at room temperature , proper disinfection can clear it up.
A 0.1% bleach contact for 10 minutes or 70% ethanol for 30 seconds contact is enough to clear these parasites. You will need more contact time such as 30 minutes if you opt for sodium hydroxide or hydrogen peroxide
Ideally, a blood test should be done to all rabbits and healthy ones should be kept in their own colony and the infected ones be treated.
For a new rabbit, consider isolation and testing. Repeat after a month to confirm it is does not have this parasite.
Always isolate and test any new rabbits twice. First when you get them and after a month to ensure they are not infected.
In case any of them is infected, treat all the rabbits you have for 28 days, clean and disinfect their environment weekly for about one month. Treatment can also be used as a preventive measure as it does not have any adverse effect since there is no vaccine
E. cuniculi in humans
Since it can affect humans, it is good to discuss something small about E. cuniculi when it affects humans since are chances you may get infected while handling your furry friends.
Not that EC is zoonotic, i.e., it can be transmitted and affect human beings. However, as already indicated, it mainly affects people whose immunity is low (immunosuppressed).
Rabbits can carry the E. cuniculi for a lifetime. It is good to ensure you put in place measures to ensure it does not affect these pets.