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About 10% of FAP j-pouchers have at least one bout of pouchitis within 10 years vs. 50% of IBD patients.

"The incidence of pouchitis is markedly different between patients with UC and FAP. In UC the quoted incidence varies from 20% to 50% between studies [Hahnloser et al. 2007; Romanos et al. 1997; Stahlberg et al. 1996]. In FAP the incidence of pouchitis is much lower than in UC and varies from 0% to 11% [Barton et al. 2001; Nyam et al. 1997; Kartheuser et al. 1996; Fazio et al. 1995; Dozois et al. 1989]"

Full article here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002591/
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I lost my colon due to high grade dysplasia. First surgery was Nov. 2, second was Dec. 28th. I've had a very mild case of pouchitis one time that three days of Cipro took care of, but have had no other issues, other than just getting used to it at the very beginning. I LOVE my pouch and am so thankful that the initial surgeon I saw (I was ready to have a permanent ileostomy) asked me to get a second opinion before he did my surgery. I DID have UC, but it was very well controlled with my medication, I never had flares. Feel free to let me know if you have additional questions.
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