Thrush is a fungal infection and is treated with anti-fungal medications. These are only available with a doctor's prescription; they are not available over-the-counter.
Oral thrush (also called oral candidiasis) -- is a condition in which the fungus candida accumulates on the lining of your mouth. Candida is a normal organism in your mouth, but sometimes it can overgrow and cause symptoms. This may happen due to a weakened immune system.
Anti-fungal treatments can be topical (i.e. only applied to the part of body that is affected) or systemic (acting on the whole body). A 'troche' or "lozenge" that dissolves in your mouth is a topical treatment. A liquid that you swish in your mouth and then swallow is another topical treatment.
Health care providers usually prefer to give a topical treatment first. It provides the medication exactly where it is needed and is less likely to cause side-effects. There is also less risk of candida becoming resistant to the medication.
Only if a topical treatment does not work will a systemic anti-fungal medication, in other words a tablet that you swallow and which brings the drug into your bloodstream, be given.
Anti-fungal medications used include clotrimazole, miconazole, nystatin and fluconazole.
More on thrush at TheBody.com
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