Hello Nicola
I am sorry that Pippa is unwell. Did the Vet also prescribe a non steroidal anti-inflammatory such as Metacam ? With cases of head tilt/nystagmus it is inflammation which causes the symptoms. So reducing inflammation is important. In the absence of a definitive diagnosis it may also be a good idea to give Pippa a 28 day course of Panacur to cover the possibility of EC. That way both bacterial infection and EC are covered as far as treatment goes.
I would see how Pippa copes if you allow her out of the carrier for a while. Sometimes over-stimulation of the CNS can exacerbate symptoms. On the other hand she may find being confined stressful. It really will be a case of seeing what she can cope with best.
I would try to bring Millie in to keep Pippa company. It may be that you will need to keep them apart when you are not there to make sure all is OK. You could have them in cages next to each other when you cant supervise them together.
Is Pippa eating and drinking OK ? Secondary gut stasis is something else to keep an eye out for.
Some Vets recommend that all Rabbits who have had contact with a Rabbit displaying symptoms of EC are all treated with a course of Panacur. Some Vets says just a 9 day course, others say a 28 day course. Personally I do the latter. It is also important to bleach clean the environment on days 21 and 28 of Panacur treatment. A 10% bleach solution can be used. Any surfaces that cannot be bleach cleaned can be steam cleaned, steam kills EC spores.
EC spores are spread mainly via the urine. So minimising the risk of a Rabbit ingesting urine contaminated hay/bedding is important to try to prevent the Rabbit reinfecting him/herself.
With regards to antibiotic treatment. With ear infections a long course of antibiotics is often needed. Also, it is often the case that Baytril alone is ineffective. Another antibiotic or an additional antibiotic aswell as Baytril may be required.
I hope that you will see some more improvement in Pippa's symptoms soon xx
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