The pathogen Encephalitozoon cuniculi causes encephalitozoonosis (also called torticollis, wry neck, head tilt) in rabbits. Approximately 80% of healthy rabbits carry the pathogen without showing any clinical signs. Mature infectious spores are mainly excreted in the urine, so that transmission takes place orally and nasally by eating infected food or sniffing at food and litter. However, infected pregnant female hares can also transmit the pathogen to their young in the womb. Faecal shedding of pathogens was detected but seems to be of little importance.

The pathogen has also been found in many other animal species such as dogs, foxes, rodents and some bird species and even in humans. Especially in immunocompromised persons, infection can be relevant.

Apart from head tilt, the clinical picture in rabbits is mainly characterised by ataxia, nystagmus, seizures or cramps. As the disease can also take a milder course, it is recommended to test for E. cuniculi in case of any neurological sign.

Encephalitocoon pogonae has been described in bearded dragons (Pogona spp.; Agamidae) and is a member of the phylum Microsporidia. Microsporidia are single-celled, intracellular, spore-forming fungi reclassified from the group of protozoa. Due to similar morphology and genetic similarities, the pathogen was first identified as Encephalitozoon cuniculi. Since 2016 it has been classified as independent species.

Infections can be associated with unspecific clinical signs including lethargy, anorexia, weight loss and polydipsia. Replication takes place in macrophages and is associated with granulomas in different tissues, especially the kidney, but also the intestine, liver, ovary, spleen, lungs, vascular endothelium, and ventricular ependymal cells in the brain. Coinfections with agamid adenovirus 1 and disease coccidia have been described, and may be associated with more severe disease.

Faecal shedding can occur and a faecal-oral transmission is likely. Diagnostic testing can be carried out by PCR and/or histopathology from the affected tissues or by PCR using a cloacal swab or faecal sample.