Antibiotics are the only way to get rid of it. But if I'm wrong, someone will definitely come along and correct me. 
The antibiotics would be harsh, but there are ways to counteract the effects, such as taking probiotics. Ultimately, it would probably be better to take them and get rid of the bacteria, and deal with setting your system straight again afterwards. That's how I see it, anyway. But anyhow, if you do a board search, no time limit, you'll find lots of helpful information about dealing with the effects of antibiotics. Good luck!
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