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Clean the skin
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Depending on how large an area of your horse is infected, you will need to bathe the affected area. Fungal infections of the skin cause small scabby areas to form under the hair follicles, creating a scaly area of skin that hurts and bleeds when you pull the scabs away. Unfortunately, to get rid of the fungus, the scabs have to go. They must be washed out, picked out, and dried out. Start with a good bath using an iodine based soap, like Betadine, and scrub the affected skin to loosen the scabs. Pull the bits away that loosen, just take care to notice the pain level of the horse. You might get a response you don't want--like a bite or a kick. It hurts! So be gentle.
Apply medicine
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Removed as much of the flaky tissue and hair as possible, apply a topical antiseptic and drying agent. You can mix two caps of bleach with some water and place it in a spray bottle and use that, or you can used a slightly diluted tincture of iodine. There are some products, like Fung-Away, you can purchase from the feed or pet supply store that you can also apply. These medicines will need to be applied daily, and make every effort to keep the skin dry and clean and relatively hairless. Once the fungus clears, the hair will come back.
Veterinary Treatment
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If the skin infection spreads or worsens, call your veterinarian. Often horses with a bad fungal infection of the skin have another underlying health issue that needs to be addressed. A fungal infection that won't go away can be a sign of a compromised immune system and needs to be checked out. Keep in mind that fungus is very hard to kill, so don't be surprised if it takes several weeks to see any major improvement.
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Horse Fungus Cure
Horses are amazing animals. Weighing up to 1,200 lbs. or more, and able to reach speeds of 35 mph, they are some of nature's more powerful creatures. For all their strength and size, they can be surprisingly delicate. Small infections can cause big problems for horses, one of these being fungal infections of the skin. Knowing how to get rid of a fungal infection is a real asset for the horse owner.