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Managing Cryptosporidiosis in a Shelter Setting


Authors: Dr. Alexandre Ellis
Document Type: FAQs
Species: Feline

Cryptosporidiosis is an often-seen parasite in cats in high stress settings. However, clinical signs are usually mild and self-limiting. Dr. Ellis explores the question, should we be aggressively treating every case of cryptosporidiosis in a shelter setting? Are there other factors that come into play?


I have an outbreak of cryptosporidiosis in two of my open plan cat rooms and I am struggling to control it. A while ago I was listening to a podcast that I think may have involved your organization / Maddie’s Fund and a couple of times it mentioned that good results had come from recent studies for treating Cryptosporidiosis. I have been searching for the reference and can't find the name of the drug.

Can you help? I do know about environmental control, but I have some sick cats (FIV/FeLV negative) that are not responding to treatment




Thank you for your question and your input on our resources! Your question is a very good one, and I hope I will be able to assist you, although your situation is a tricky one.

Unfortunately, there is no miracle drug that treats Cryptosporidium in cats, although we wish there was! Of the few treatment options that exist, none have so far demonstrated constant elimination of the parasite. The Companion Animal Parasite Council is a great resource for veterinary parasitology recommendations. CAPC’s cryptosporidium guidelines were most recently updated in April 2017 and can be found here:

Paromomycin is a medication that has been used with some success according to CAPC. In many cases, diarrhea caused by Cryptosporidium will also improve with a gastro-intestinal diet as well as probiotics.  

If possible, I would like to have more information on the testing done so far and clinical signs of your cats. Is it limited to diarrhea or have you noticed other signs such as anorexia, weight loss, vomiting, etc.? Because of new testing available, mainly PCR, Cryptosporidium is more frequently diagnosed in cats, and, in most cases, it will not be the primary cause of clinical signs. If an animal tests positive for Cryptosporidium but does not have any clinical signs, treatment is not recommended.

In most cases, Cryptosporidium will be an opportunistic pathogen and will rarely cause diarrhea by itself, so it is recommended to screen for other parasites (Isospora, Tritrichomas, Giardia, etc.) and diseases. We would recommend, if it has not already been done, a medical work up to include ruling out other causes of chronic diarrhea. Stool sample analysis by a laboratory would be indicated, as well as making sure animals have been dewormed against more common parasites of cats. A combination of Ponazuril and Fenbendazole is usually recommended in cases of refractory diarrhea.

It is also important to address how crowding, stress, and sanitation might be contributing to feline diarrhea and recurring parasitic infections in the shelter. Crowding leads to prolonged lengths of stay (LOS), increased stress levels, greater risk of disease introduction and exposure, higher risk of contact between animals, and, often, compromised housing and husbandry.  Strategies to alleviate crowding and stress include moving kittens to foster or adoptive homes ASAP, functioning at your true capacity for care (C4C), ensuring appropriate floor space in group housing areas (18 square feet per cat), cage space for cats housed singly (preferably compartmentalized), and spot cleaning all cat cages with adequate cleaning/disinfection protocols.

As you mentioned, Cryptosporidium is very resistant in the environment and is resistant to most disinfectants. One of the most important ways to reduce environmental contamination is by mechanical cleaning to physically remove as many oocysts as possible from the environment. Disinfectants applied to a pre-cleaned surface are more likely to be effective against resistant pathogens in general.

I hope I could provide some help. Please let us know if you have any other questions.

Best wishes,

Alexandre Ellis, DVM
Maddie’s Fund Shelter Medicine Resident
Shelter Medicine Program
University of Wisconsin – Madison
School of Veterinary Medicine