You might be able to prevent cuffitis flares by using rectal mesalamine (e.g. Canasa suppositories or by enema). It's probably helpful not to think of either of these as infections. Cuffitis especially is just like UC in the small remnant of colon that you have (the "rectal cuff"). Pouchitis seems to be connected to the bacterial mix in the pouch, and antibiotics alter that mix - but it's not an ordinary infection.