E. Cuniculi

TIP – Prevention is the best method but if you suspect your bunny has E. Cuniculi you must get it to a vet as soon as possible.  The earlier the treatment the better chance of stopping further symptoms.  If you suspect your bunny has E. Cuniculi & you can’t get to the vets quickly, give them a dose of Panacur, this will hopefully slow down any damage from the parasites.  If it isn’t E. Cuniculi the Panacur won’t do any harm.

E. Cuniculi, it’s full title Encephalitozoon Cuniculi, is a protozoan parasite.  A microscopic parasite of the brain & kidneys.  Some rabbits can carry the parasite with no effects but can pass it on.  The parasite causes lesions on the brain & other organs.

How it is Transmitted

The parasite can be passed on through spores in the infected rabbit’s urine. If a non infected rabbit shares the same grazing area as an infected rabbit there is a possibility that the non infected rabbit will eat the grass which has been contaminated by the urine of the infected rabbit. Unborn kits may also receive the parasite from their mother.

It has been said that the parasite is common in domestic & laboratory rabbits but very rare in wild rabbits. To date I have not been able to find any information as to the reason for this.


  • Head tilt.
  • Seizures.
  • Eyes flicker from side to side.
  • Weakness in the legs.
  • Spinning round or rolling over.
  • Cataract.
  • Deafness.
  • Drinking & toileting more.
  • Behavioural changes.


Prevention is the best method but can be costly. This is done by testing all current & new arrival rabbits via a blood test. However, the blood tests may not show recent exposure.
The treatment for your rabbit will all depend on what symptoms they are showing, so only by you & your rabbit visiting your vet will you be able to determine what that is.
A common treatment is to treat your rabbit with a 28 day course of a rabbit wormer.  This has been known to help put the parasite into dormancy, you can’t kill the parasite as it’s within the bunnies cells.  The only wormer that I am aware of for use in rabbits is Panacur which contains Fenbendazole & is in the form of a paste.

Panacur – Wormer for rabbits.
It is administered by a graduation system from a tube & is a paste.

My Experience

I believe I have had a couple of bunnies with this back in the 90s, as I remember the head tilt, flicking eyes & the leg weakness.  Unfortunately, non were diagnosed with E. Cuniculi, in fact no diagnosis was given.  Their symptoms were treated but both died.

Kitty in her prime.

One of my worst experiences was with Kitty.  Kitty was a German Lop, which is a large breed of rabbit, & her problems started at the age of 6 years. She had a lot of complex problems.  Not all were caused by the E. Cuniculi. Her problems were:

  • Runny eyes caused by a kink in her tear duct.
  • Behavioural issues. In hindsight I think this was due to the E. Cuniculi.
  • Burst ear drums.
  • Frequent bouts of soft faeces.
  • Build up of ear wax.
  • Suspected slightly deaf.
  • Arthritis.
  • Soiling her back end with urine & faeces.
  • Poor coat condition & frequent matting.  This was in part caused by her arthritis.
  • Cataracts that lead to blindness.  This was caused by the E.Cuniculi.
  • Fast heart beat.

All of these problems did not start at the same time.

Treatment of Kitty involved a very high maintenance program which went as follows:

  • Runny eyes – Frequent tear duct flushes, regular eye drops, daily cleaning of the eyes & de-matting of the fur around the eyes.  Also applying a protective barrier on her skin where the tears were making it sore.  I used Vaseline.
  • Behavioural issues – this was dealt with by dealing with each health issue one by one, giving her a break & a little treat after each treatment. If she bit me or attempted to I would walk away,  leave her for a minute, not give her a treat & do another treatment.  I would also reassure Kitty & spend time just stroking her or talking to her as I felt some of her behavioural changes were down to fear.
  • Burst ear drums – Antibiotics.
  • Frequent bouts of soft faeces – I would treat her with either Protexin, Fibreplex or Pro Fibre.  All are probiotics. I had the most success with the Profibre pellets long term.
  • Build up of ear wax – Regular checks in her ears & an ear flush.
  • The suspected deafness I dealt with by making sure she could always see me & I took it slowly when approaching her.
  • Arthritis – Twice daily doses of Metacam, an anti inflammatory.
  • Soiling her back end – Baths as & when required but for the most part this was kept under control by the Metacam as it helped her arthritis so she could lift herself properly when toileting.
  • Regular grooming & de matting.
  • Cataracts – Always approached her slowly trying to make loud enough noises so that she could hear me. Kept her pen the same layout & always placed her water & food dish in the same place.
  • Fast heart beat – No treatment.

As Kitty grew older the first problems to manifest were her age related problems. The runny eyes became worse because her teeth had sunk & shifted position.  This resulted in the roots of her teeth pushing against her tear duct causing a kink so tears could not flow away as normal.

Kitty at a young age with no eye problems.
Kitty at an older age with chronic eye problems due to a kink in her tear duct.

Kitty also had a large build up of ear wax in just one ear & we thought this was contributing to her deafness.  During a tear duct flush the vet also flushed her ear.  At first just normal brown wax came out but was soon followed by a white rubbery material.  Whenever she had to have a sedation or anaesthetic I always took the opportunity to ask the vet to de matt the areas I struggled with. A lot less stressful for both of us.  After these procedures had been done Kitty was a lot brighter & lively.  She had to have ear & eye drops for a time afterwards. She also seemed to be able to hear slightly better.  However, it was at this point her behaviour started to alter. She became more aggressive towards me & the other bunnies including her partner. She would bite on a regular basis.

It was about a month later at a morning feed, I found Kitty was unable to walk, her eyes were flickering & she had no motor control.  I have to admit it was a scary & distressing sight.  I immediately got her to the vets.  Her ears were checked & they were both full of pus.  The vet suspected her ear drums may have burst.  We could not flush the pus because you would never flush an ear if the ear drum is suspected to have burst. The liquid used in the flush would cause more damage & make it worse.  Kitty’s symptoms corresponded with a burst ear drum diagnosis.  She was immediately put on to an aggressive course of antibiotics.  This was by injection twice a day for as long as needed. The ear drum should repair itself but can take a long time.  Once home she had to be confined so she didn’t injure herself.
A few days into the treatment & Kitty deteriorated, her breathing seemed fast, still not eating well only veg, she was producing soft faeces & her tears were now milky & the consistency was getting thicker. I took her to the vets & her heart was fine & she had made some improvements, her eyes no longer flickered, she had control again of her mobility & she was reasonably bright.  It made no sense that her milky tears were getting thicker with being on such an aggressive course of antibiotics.  Her weight loss was a huge concern & she wasn’t going to be able to take much more loss.  It seemed the infection was not going.
It was suspected that she might have an infection in the head.  She was to continue with the antibiotics, restart the Maxitrol eye drops & start Metacam. We would reassess in a few days. If this didn’t work it was not looking good.

I started to provide intensive care to Kitty.  Making sure she would eat something was a priority.  I started with veg, grass, forage & fruit & put her on some probiotics to help counter the antibiotics.  Anything to keep her guts moving.  I fed her little & often throughout the day.  This worked & we had stopped weight loss, she was looking brighter too. However, we would have good days & bad days, why this happened we don’t know but as long as overall she was improving then it was good. Her milky eyes started to go back to clear tears & the pus reduced in her ears.  It all seemed good but then she stopped eating so it was back to the vets. The vet was actually surprised how well she was doing.  Her heart & lungs were all fine, hardly any pus in her ears which suggested the infection was on the way out, no lumps felt inside her & she was bright & lively as she got to explore the surgery room. The only real issue now was her eating & this was due to her having the good & bad days.  In humans any ear or balance issues can make a human feel nauseous so maybe it was the same for Kitty, however, that was just speculation as it is not known if rabbits can feel nauseous especially as they cannot be sick. She was given a gut stimulant & I had to keep up the food regime. For the next 10 days Kitty had good & bad days but more good than bad.

It was time for a visit back to the vets for an assessment.  Kitty’s balance had improved further, no pus in the ears & her weight had gone back to what it was before which was a huge relief. Kitty’s behaviour halfway through the treatment had improved too.  She coped with the handling & medicating really well & only on the odd occasion did she try to bite.  She was still not out of the woods & the antibiotics had to continue for another 2 weeks. Over the coming months Kitty got back to normal except for the odd blip in eating.  She had a check at the vets & it was confirmed the infection had gone.

However, 2 months later her behavioural issues returned with a vengeance.  She was very difficult to handle. Her runny eyes, matted fur & soft faeces were also a constant battle.  Her eating was also very up & down. We did manage to stabilize her with Metacam as the lack of eating seemed to be caused by her arthritis pain.  We kept her stabilized over the coming winter months but as Spring approached Kitty never returned to normal.  Her soft faeces were a constant issue so she came off the Metacam as this could have been a cause.  It didn’t help. She also developed a slight head tilt, was excessively drinking & her arthritis was causing her issues. After a discussion with the vet it was decided Kitty was to have a blood test. I booked her in for the following day but overnight she went blind. It was a shock.

At the vets it was established the eyes had cataracts on them & the right eye also had an ulcer. The cataracts were identical which is unusual & also the speed at which they have occurred is also unusual. It appeared that it was not just the lens that was affected, which is normally the case with cataracts,  but in front of the lens too there were white lines. The vet confirmed Kitty was totally blind. It was right to stop the Maxitrol drops, I stopped them as soon as I realised she was blind, as they are a steroid eye drop & they shouldn’t be used on ulcers. The Fulcithimic cream would be ok as non steroidal.
Kitty had her blood taken & it was tested for organ function.  But also because of the head tilt & blindness we requested a test for the E. Cuniculi.  It was suspected something was going on inside her as a lot of the symptoms pointed to that.  If the antigens are running high in her that can affect the eyes, too much protein can too. Really we wouldn’t know until the blood test results came in. All in all her overall condition with everything going on was actually pretty good.

Kitty’s results came back & there was good news & bad news. Firstly, her normal blood test showed that her kidneys & liver were ok but there was a low degree of anaemia, this  meant that a disease had been grumbling on for a while. Her E. Cuniculi tests were in two parts, the first was initial exposure & her results were normal, the second part was long term exposure & unfortunately Kitty’s results were high. The ranges were:
1 in 80 = Normal.
80 – 160 = Possibly.
320 – 640 = Likely.
640 – plus = Very Likely.

Kitty came in at 2500!

I’m not totally sure how the results are worked out. Reading other people’s experiences with the disease Kitty didn’t seem that bad even if her results were very high. It’s most confusing & the opinions out there differ significantly. This is where you need a good vet & one you can trust.

Kitty had started to improve but was put on Panacur, a rabbit wormer, for 28 days in the hope it could cure her. This isn’t guaranteed though. The first couple of days Kitty showed improvement, her eating was good & she gained weight.  I also managed to get her guts under reasonable control too.  However, on the third day I noticed she was urinating on her back legs.  It was decided to restart her Metacam as after a discussion with the vet it appeared her arthritis was causing pain again. Kitty’s daily routine went as follows:

Morning -a comb, de matt, eye drops, Vaseline applied & a dose of Metacam.
Lunch –  hay fed as normal, she was eating a lot & a water top up.
Late afternoon – eye drops again & the final dose of Metacam.
Evening – a dose of Panacur on a treat (rich tea biscuit sandwich).

Her biggest issue was the wetting herself & her runny eyes. The problem was both conditions were making her fur matt. She had really thick dense fur which caused her to feel hot & the fur to matt easily. In fact the problems were matting her fur to an extent that it became impossible to keep on top of, even though I had drafted in help from other people. She was starting to smell too. Her ear started bothering her a bit more but her eating was very good. She was drinking a little more but it seemed to be up & down. Kitty had improved slightly before the Panacur wormer & the head tilt didn’t seem to have been affected by the wormer so I don’t know whether to be convinced the Panacur was doing her any good or whether her body was doing it on it’s own.

Kitty used to hunt out cool places. The garage being her favourite place.

I was bathing Kitty on a regular basis  & was able to get a lot of urine stain off her but I now started to find some sores.  The skin was very red & had bits of pus round the edges & over the top. I applied diluted Hibi scrub. I contacted the vet & he agreed we should raise her Metacam dose to the original 15 & hope that stops her urinating on herself. As for her weight that was good & she must feel good to be eating. Told him about the sores & I checked ok to continue with the Hibi Scrub.  I explained I was struggling with her fur so he  suggested a different type of brush.  I gave it a go but it didn’t really help significantly.

A few days later I took her back to the vets as I wasn’t so sure it was fair to keep her going, she wasn’t improving & seemed unhappy. She had lost weight & she was now walking rather than hopping. Her constant wetting herself, the vet said was more to do with her sitting in her urine & why she is doing that we do not know. It is possible with her being blind she just doesn’t want to get up & go somewhere. Since she had gone blind she was urinating anywhere but the only time I saw her sat on it was if there was hay there. The Metacam had made no difference & her sores were starting everywhere underneath her near her urine area. I was struggling to maintain her & the vet said anyone would as it’s not easy to keep on top of such a huge amount of matting fur. He could see a deterioration in her & he asked about her heart rate. I said I had seen her breathing faster than normal over the weekend. He listened & said her heart was beating that fast it was almost tripping over itself.  All in all her quality of life had deteriorated & everyday will be worse than the day before. There was no going up from this. The medication was not working either. I felt it was not right to keep her going & put her through any suffering. So I decided to let my big girl go.

Kitty relaxing.

What I learned from my experience with Kitty is to routinely give Panacur to any older rabbits & any that have a weakened immune system.  By doing this I hope to keep the E. Cuniculi parasite at bay. So out of my current bunnies that is all the oldies.

In the future I will also pay more attention to any behavioural changes & if any have soft faeces on a regular basis then I will go straight for a blood test always including the E. Cuniculi test.