Parasitic Infestation: Encephalitozoon Cuniculi in Rabbits (What It Is, Symptoms & Treatment)

Parasitic Infestation In Rabbits

For rabbit owners, the wellness and health of their pets is important because this ensures that they will live longer without suffering from any health risks that can threaten their life. 

That means that taking good care of your rabbit does not only mean giving them quality time and bonding but also ensuring that they get to eat the proper types of food that are suitable for them and get to live in an environment that is safe and clean.

But of course, the most important is ensuring your pet is free from any sort of illness. One such health condition you should look out for is Encephalitozoon cuniculi. According to some reports, this kind of parasitic infestation is commonly diagnosed in an indoor or captive rabbit. 

That is why rabbit owners should keep an eye on this infestation and be wary because it can potentially lead to more serious health risks. 

Encephalitozoon cuniculi

Some rabbit owners commonly mistake Encephalitozoon cuniculi for an illness or health condition affecting their pet. However, this type of microscopic parasite can cause infestation if left untreated. This parasite can potentially damage your rabbit’s kidneys and brain. 

The National Library of Medicine stated that what’s alarming about this parasite is that it can be transported and infect humans at times and may cause harm to animals other than your pet rabbit.

Many different rabbits have Encephalitozoon cuniculi in their bodies without you knowing that. In some cases, the rabbit already has this parasite and will not show any signs of disease.

However, you should know that Encephalitozoon cuniculi are one of the biggest reasons for many diseases that affect rabbits. As such, you should ensure that your rabbit is as free of this parasite as possible.

Life Cycle of Encephalitozoon cuniculi

It takes three to five weeks for  Encephalitozoon cuniculi to complete the incubation period in their host. There are different stages on how your rabbit can get affected.

  • First– Your rabbit will inhale spores with the E. Cuniculi parasite.
  • Second– After successfully finding a host, they will attack and live on the surface inside their body and grow as mature parasites. 
  • Third– They travel through the body to infest your rabbit’s cells.
  • Fourth– Infected rabbits will urinate that contains parasitic bacteria
  • Fifth– New E. Cuniculi will wait to infest a new potential host nearby. 

To better understand how E. Cuniculi is formed, look at the table below:

CycleCycle Description
1st cycleIngestion or Inhalation of Spores
2nd cycleTransplacental Transmission
3rd cycleHost cell rupture and grow as a mature parasite
4th cycleSporoblast Synthesize E. Cuniculi Spore
5th cycleSporonts become Sporoblast
6th cycleMeronts convert to Sporonts
7th cycleMeronts undergo several replications by binary fusion
8th cycleSporoplasm divides to create meronts
9th cyclePolar tube penetrates cells and passes sporoplasm and nucleus 
10 cycleSpores are excreted in urine or fecal of the rabbit
Then it will repeat the cycle

Encephalitozoon cuniculi Transmission

Now that you know what danger parasites can bring to your rabbit’s health, the next thing you should know is how it is transmitted to your rabbit and other species.  Rabbit Welfare Association and Fund stated that exposure to one rabbit to Encephalitozoon cuniculi could lead to a possible transmission to the whole herd or other nearby species.

Since it is quite common for most rabbits to have this parasite in their bodies because they are more vulnerable, microorganisms and bacteria are pretty easy to transmit from one rabbit to another. 

While a few of these parasites probably won’t affect your rabbit severely, you should not overlook and leave the infestation untreated because they can lead to serious diseases and illnesses.

The main way for Encephalitozoon cuniculi to infect a potential host is through spores in urine. That is why cleaning the litter box, and cages are important because many bacteria and parasites live on the surfaces. Also, sometimes when your rabbit is urinating, some of their pee splashes and contaminates its drinking bowl. Hence, if your rabbit shares the same bowl, rabbits can pick this parasite up when it drinks water contaminated with the spores. 

Although in some cases, pregnancy can also transmit the parasite. This can happen if the mother rabbit is infected by encephalitozoon. Baby rabbits will already have Encephalitozoon cuniculi in them before they are born. 

As a rabbit owner, keeping your rabbits safe from Encephalitozoon cuniculi is important because even something as simple as drinking water and pregnancy can easily transmit the parasite to your pet and you. 

Encephalitozoon cuniculi Symptoms

If you want to know whether or not your pet rabbit has Encephalitozoon cuniculi, here are the symptoms you should keep an eye on


One thing that you should look at is the possible infection in the rabbit eye. Check the eyes because Encephalitozoon cuniculi spores can travel in your pet’s eye and multiply their number on its surface. This can potentially lead to cataracts and even something so simple as your rabbit’s eyes tracking from side to side.

Head tilting 

Another indication of Encephalitozoon cuniculi infestation is that your rabbit will tilt their head constantly. . That is because this parasite can attack the neurological system that can lead to diseases concerning neurons of the body. It also affects the rabbit’s control over its basic bodily functions. As such, it will be common for your rabbit to involuntarily tilt its head over to one side due to the neurological disease caused by Encephalitozoon cuniculi.

Weakness of the Legs

Sudden weakness of your rabbit’s leg is also an indication of the presence of Encephalitozoon cuniculi because of how a neurological disease may cause them to be unable to properly control its legs. At times, this can even lead to paralysis in the legs.

Other similar symptoms related to neurological diseases are uncontrollable and sudden spinning and rolling. Seizures can also happen if the condition gets worse.

Increase/Decrease in urination.

Suppose your rabbit is urinating more than it usually does and is more likely to drink water. In that case, there is a chance that it also has Encephalitozoon cuniculi because of how this parasite attacks the kidney system of your rabbit. Hence, the urination activity of your pet will be affected. 

Weight Loss

Like other parasitic infestations, E. Cuniculi cause sudden weight loss in rabbits because they also lose their appetite to eat. Even if you fodder them the usual food they are eating, the uncomfortable feeling inside their body motivates them not to eat and just rest inside their cage. 

Diagnosing Encephalitozoon cuniculi

Since Encephalitozoon cuniculi is a parasitic infestation that sometimes has severe symptoms for your rabbit, the best way to diagnose them is by visiting your pet’s doctor. 

It is not recommended at all times to diagnose and provide home remedy treatment for your rabbit by yourself without the assistance or the help of a veterinarian because Encephalitozoon cuniculi can also infect you or cause serious diseases in other animals.

In diagnosing this infestation, doctors usually do a ‘fingerprint’ test using a microscope to detect the presence of Encephalitozoon cuniculi in the rabbit. However, there are other ways to determine whether your pet is infested.

  • Blood Test

One of the easiest ways of determining parasitic infestation and known diseases in rabbits is by getting their blood sample. According to MulberryVets, blood cells contain antibodies and help doctors determine whether there is a decrease or increase in red blood cells (RBC). With that, doctors can easily identify active infestations inside your rabbit’s body.

  • Urine Test

Urine test is another way to identify E. Cuniculi infestation because the parasite’s spores sometimes lie on the surfaces of the kidney. That is why one of the health risks of having this kind of parasite in your rabbit’s body is damaging its kidney and affecting its urinating activity.  

  • Stool Test

Your rabbit’s poop tells a lot about its health, and any change in the texture, appearance, or consistency of its droppings can indicate that your rabbit is experiencing an unhealthy digestive process or some parasitic infestation. You can send a fecal sample by getting their latest dropping and putting it in an enclosed container. It’s easy to identify the presence of E. Cuniculi in poop because it is part of their lifecycle, attaching their spores in the stool to be able to find new hosts nearby.  

Encephalitozoon cuniculi Treatment

Treatment should only be done after seeing a vet and getting the proper diagnosis for your pet rabbit. Although there are a lot of suggested home remedies that you can read, your pet’s doctor provides the best way to treat them. You should never treat it on your own without the supervision of a professional because of how serious this condition is and how it can potentially lead to further health risks for you and your rabbit. 

Because of how small Encephalitozoon cuniculi is, most treatment options are non-invasive. Instead, vets will prescribe medications meant to reduce and treat inflammations in your rabbits. Anti-inflammatory drugs such as steroids may be prescribed. 

Moreover, some treatments aim to kill off the Encephalitozoon cuniculi in the rabbit’s body. That is why anti-parasiticides are also given as a way of helping the rabbit recover. Both anti-inflammatory and anti-parasiticides should be given daily for about a month, depending on what the vet prescribes and the severity of the infestation case. 

Key Takeaways

  • Parasitic Infestation commonly happens in captive and indoor rabbits. One infestation that can occur to your rabbit is the Encephalitozoon Cuniculi which can potentially damage your rabbit’s kidneys and brain. 
  • Rabbits’ bodies are the common hosts for this parasite because they are more vulnerable. However, this kind of parasite is transmittable to your rabbit pet and can affect humans and other animals nearby. 
  • The incubation period for E. Cuniculi takes three to five weeks to complete. The first step is finding the host. Second, finding a cell or surface to grow their number. Third, attack the body surfaces like your rabbit’s kidneys and nervous system. Fourth, the spore of the parasite will stick to the urine or poop of your pet. Last, after excreting body waste, they will find potential new hosts nearby. 
  • The common symptoms you need to keep an eye out for parasitic infestation are cataracts, head tilting, sudden weakness in legs, increased/decreased urinating activity, and weight loss. 
  • Never self-diagnose your pet with the information that you just read online. There are professional ways for veterinarians to get samples of the active parasite in their bodies. Such as blood tests, urine tests, and stool tests. 
  • A veterinarian gives the recommended treatment for E. Cuniculi. They prescribed anti-inflammatories and anti-parasiticide medicine, but it will depend on the severity of the infestation of your rabbit. 

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