I am actually allergic to flagyl! My throat swells, I get hives everywhere. It's horrible. Cipro is a good second choice but doesn't completely eliminate the pouchitis. For the bout of pouchitis that I am fighting now, which has been the worst I have ever experienced in 16 years, my GI wanted to try a combination of Levothyroxin and Augmentin. But I have to take them separately because, as I have found out, I will just throw them right up.
So far so good. My bum is feeling better, the use of pain meds is decreasing and I can actually move without the urgency to go to the bathroom.