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Coccidia is a protozoa that is often present in very low numbers in healthy reptiles and is only a concern when the levels become more than just a few on a fecal float slide.  The most common symptom of Coccodia is feces with an unusually bad smell that could "clear a room."   Reptiles with untreated Coccidia will eventually stop eating and appear listless.  Coccidia prevents absorption of nutrients and normally well-fed reptiles with higher numbers of Coccidia will not appear healthy or might begin to have a thin, malnourished appearance. 

Coccidia is often acquired from infected feeders, and most commonly can be found on the outer shell and legs of feeder insects.  Leaving feeder insects in your reptile's enclosure with fecal matter will increase the risk of coccidia infestation, as the feeders will often contact the fecal matter or ingest it, and then the reptile eats the feeder, and the coccidia then enters the reptile.   Coccidia is easy to treat with anti-protozoal medications which can be obtained by your veterinarian.  In order to diagnose Coccidia, your vet will perform a fecal float and look at the slide under a microscope.  He will then determine the number of
oocysts that are on the slide and decide if they are in high enough numbers to treat the infestation, and what medication would work best. 

During treatment, it is very important to maintain a clean enclosure for your reptile.   Often it is advised to remove all furnishings and use disposable furnishings, to keep fecal matter from contaminating the environment and reinfestation of coccidia.  Disinfecting of the enclosure is extremely important during and after treatment for Coccidia and it is recommended to use disinfectants such as Quarternary Ammonia Compounts or Ammonia Chloride cleaners.  Leave the disinfectant on the surface of the enclosure for 15-20 minutes to ensure that it has time to be effective.  It is advised to spray the disinfectant onto the surface rather than use a porous applicator such as a rag or sponge, to ensure complete coverage of the disinfectant onto the surface.   With disinfectants it is important to rinse the enclosure well before returning your reptile to its home.  Soak any tank furnishings in the disinfectant for 20-30 minutes and rinse and dry well prior to placing back in the enclosure. 

Below are some informational links supporting the above information, as well as additional cleaning recommendations.

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Ivan Alfonso, DVM explains Coccidia in reptiles and has some slides from fecal floats showing what Coccidia looks like.
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Reptile Community.com's page on Gastrointestinal Parasites explains Coccidia and its treatment.
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Beautiful Dragons has outstanding information about parasites and medications, including dosage charts.  This page explains the relationship between feeders and parasites.
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Fire and Ice Dragons article titled - Bearded Dragons and Parasites explains common symptoms and treatments of parasites, including Coccidia.
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Reptic Zone forum thread with helpful information to support bearded dragon owners with questions about Coccidia.