Daniel, it might well turn out to require antibiotics long-term, but there are some other things worth trying before coming to that conclusion. Have you tried VSL #3 DS in significant doses? It's expensive, but it can help prevent pouchitis from recurring, or at least delay recurrences. Also, some people get good results by significantly reducing their carbohydrate (sugars and starches) intake. If you can manage that it might provide a surprising amount of help. Good luck!

I have the same fear for my son. His experiences sound very similar to yours (except he is now diagnosed with Crohns). He is 3 months post takedown, they started him on Flagyl for pouchitis but after almost 2 weeks it didn't have any effect at all. I asked his doc if he could try Cipro and within 12 hours of his 1st dose he had significant results. He was having 12-15 bm's thru the day, 3-4 at night with accidents...and is now down to 5-6 per day with 0-1 at night and no accidents. He had a fever on the same day that I started Cipro and the fever went away and hasn't returned. I am afraid that when I stop the Cipro (they gave him a 14 day course) he will flare right up again.

They have no idea why he had the fever. They admitted him with the assumption that the fever would persist, they were going to do an MRI to r/o an abscess. But since the fever resolved, they didn't do any imaging and just said to continue to monitor him. I think the Cipro either knocked out whatever bug was brewing or is temporarily treating an abscess. Either way, the Cipro is doing SOMETHING positive so I am very anxious about stopping it.

I'm on Cipro long-term, and I've had great result with few side effects. Nevertheless, it's well worth exploring whether it's necessary in each case. Most cases of pouchitis really are cleared up with a course of Cipro or Flagyl, and they just don't come right back. It's also worth considering whether some gentler options (like VSL) can reduce or eliminate the need for antibiotics.