Bacteria growth/infection where stomach was stapled off?

I am 2 1/2 years postop and have been having problems w/gas and diarreah for about 4 months now. I had an emergency appendectomy in November, and a colonoscopy in December. The doc thinks that the area where my stomach was stapled off and the part of my intestine that's not being used have accumulated bacteria, which led to infection. She thinks that caused the problems w/my appendix and the gas and diarreah. (sometimes it's not diarreah, it's just loose and very frequent bowel movements, mostly in the a.m. and sometimes in the middle of the night) I was given 2 weeks of amoxicillin and it seemed to clear up for a few weeks. Now the symptoms are starting to return, so I was put back on amoxicillin. I requested that they do a stool sample to make sure that the infection they suspect is actually the problem, so I will be taking care of that in the next day or so. Has anyone had this type of infection, and if so, did it take awhile to clear up? I'm starting to get concerned. I appreciate any responses - thanks!!

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