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Treatment
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Treat the thrush topically using a thrush medication purchased from your local tack or feed store (Thrush Buster is a good one), diluted bleach, tea tree oil or oregano oil. If you don't have access to a tack or feed store, purchase a thrush medication from an online retailer like Jeffers Equine (jeffers.com). Some people avoid the diluted bleach solution because of the possibility of it splashing onto you or your horse's skin.
To make sure the treatment you choose gets into all of the crevices of your horse's hoof where the bacteria are, wrap sheet cotton around a hoof pick, then soak the cotton in the treatment. Use the hoof pick to swab the cotton over the frog (the V-shaped middle section of the hoof's underside) and into the crevices along the side of the frog. Replace the used cotton with clean cotton when it darkens and continue until the cotton stays clean-looking. Consider swabbing the hoof with hydrogen peroxide before applying the treatment to get more oxygen into the area.
Prevention
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To keep your horse from getting thrush again, keep his stall clean and well-bedded. Your horse's stall needs enough bedding to soak up any urine he produces overnight. Keep him out of perpetually muddy paddocks, or fix your farm's drainage so that so much mud does not build up. Picking manure out of paddocks can help, too, as standing in manure and urine contributes to the development of thrush in your horse's feet.
Horses with small feet, long-toe, low-heel syndrome or heels that are too high are more prone to thrush. (Long-toe, low-heel syndrome is where the horse's hoof angle is smaller than the angle of the horse's pasterns.) You can't do anything about naturally small feet, but changing the horse's hoof angle can help with long-toe, low-heel or heels that are too high. For this, you may need to change farriers.
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Over the Counter Cure for Thrush
Thrush is a hoof condition in horses caused by the bacteria Spherophorus neaophorus that produces a black-colored discharge and a noxious smell. Fortunately, most horses with thrush don't go lame; the thrush must be advanced for lameness to occur.