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I have been having watery output for 5 months now . I took flagyl for a week on 2 different occasions but it did not help. My GI for 14 years retired and I am seeing a new one.
He has ordered a lot of blood tests and stool tests for different bugs like norovirus etc

He said if cultures are negative then it could be Crohn's  . Originally I was diagnosed with UC. But he said as time passes by usually people with UC develop Crohn's . I am really scared .
Could it be just pouchitis? How can one tell the difference if inflammation is present in the pouch ?

Last edited by meghspd
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You can only tell from a scope with analyzing samples what it looks like. UC-like inflammation is usually limited to the upper layers of the intestinal wall, and it is located especially at the rectum cuff or in the pouch, sometimes also way above the pouch into the small intestine.

Crohn's can affect scattered locations of the small intestine also, there is sometimes a stricture or a fistula.

There are already several posts in this forum about that subject. In the end it does not matter how you call it, my GI uses the term 'colitis indeterminata'.

Watery output for such a long time may be pouchitis (inflammation) or just IBS / IPS, but it is likely linked to bacteria. If Flagyl alone does not help you, I would try a combination of Cipro & Flagyl, that's what I was given almost every time in such a situation.

Probiotics may also be helpful, but not for everyone.

. I am really scared .
Could it be just pouchitis? How can one tell the difference if inflammation is present in the pouch ?

I am not sure I understand this. You seem to be concerned about and caught up in labels. The labels do not matter. When you say "just pouchitis"- pouchitis is bowel inflammation, just like Crohn's is bowel inflammation. Both are NOT GOOD, both need to be treated, and the treatments are exactly the same. Untreated pouchitis or treatment resistant pouchitis is just as concerning as untreated Crohn's or treatment resistant Crohn's. My GIs, and most other modern GIs who understand 2023 medical science, will tell you that the labels make no difference, at least for treatment purposes. I have been an inconclusive diagnosis for 15 years. DO NOT spend time, money, or energy chasing a definitive diagnosis.  Just treat the inflammation and focus on that. Choosing a correct label for it simply doesn't matter. As Steve G mentioned above, call it "indeterminate ileitis" if you need to call it something. That's what I am, as far as an operative diagnosis.

I have inflammation in my ileum and have been treating it successfully for 15 years, and have had a J Pouch for 30 years (inflammation first appeared in ileum in 2008). I spent years chasing a correct diagnosis and none of it mattered in the end because it didn't and wouldn't change a thing. You have what you have. Treat it and hopefully the treatment works.

Further to Steve's post above- it's true that fistulas are typically associated with Crohn's and they are a concern. Although I may be a Crohn's diagnosis (unknown for sure and we will never be sure), successful treatment has likely prevented appearance of any fistulas. Fistulas also could arise as a result of inflammation in the pouch.

Last edited by CTBarrister
@meghspd posted:

He said if cultures are negative then it could be Crohn's  .

This testing and all other diagnostic testing is notoriously unreliable, and if you are told otherwise, don't believe it. Spend money looking for a "correct" diagnosis at your own risk- see my post above. You would be better off spending your money on lottery tickets, although a wiser decision would be to invest it in treatments of the indeterminate ileitis (which treatments are exactly the same for Crohn's, pouchitis, indeterminate colitis, indeterminate ieitis, IBD #9, or whatever the heck else you might want to label it).

Last edited by CTBarrister

@Scott F, @CTBarrister

Thanks a lot for all the info. I will go through previous posts.

This is a new GI doc. My previous one retired so now back to square one. So, I am having little bit of trust issues. He has lot of experience in IBS/IBD. He is older ( 74years). I thought I will take his opinion due to his experience and body of work. But, he seemed non emotional and non empathetic .
He just said we will do stool test if not then pouchoscopy. He said he is afraid I have develop crohn's as lot of people eventually end up getting it after maybe 5-7 years  of jpouch .
He has ordered lot of stool tests : stool culture , norovirus, rotavirus , even some tbvirus test. This is the first time I am doing so many stool tests . My previous GI use to order stool culture only .
He said, if its Crohn's, then I would need stronger meds and it felt like he was suggesting biologics or immuno suppressant's. I do not want to jump to biologics before trying different antibiotics than flagyl .  So, thats what I am worried about. Initially, the treatment might differ for pouchitis  vs Crohn's.

I have started taking generic align as I cant tolerate even little bit of lactose. This one doesn't have any and it has reduced cramping. But I still have watery output especially if I eat protein . I do better with rice, bread, bananas and cooked veggies. But I could eat everything without issues 5 months back. I use to have well formed stool and did not need any meds not even Imodium.


I am not necessarily looking for label but more concerned about the treatment.
I don't want to go on biologics unless its the last resort as I didn't do well with them while on UC and had bad side effects.

Also , if its Crohn's then it wont be limited to pouch. It could spread throughout the GI tract. So again, treatment could be different.

I also got peripheral neuropathy when on Cipro. Had tingling and numbness in legs and abdomen. So, I was advised to not take it.But maybe, I will try it again and see if it helps and I can tolerate it. Or may be try some other antibiotic  or meds before immuno suppressant's and biologics.

Thanks a lot, again !

Last edited by meghspd

I had a stool test very recently and my GI was amazed by the results- it showed no markers for inflammation. Yet I have had inflammation in my J Pouch for 28 years, and in my ileum for 15 years.

While it's true inflammation can spread, it doesn't if it's treated effectively. I have treated pouchitis/Crohn's whatever you want to call it for 28 years, first with antibiotics and now biologics. My quality of life is excellent. I have worked as a trial attorney for 30 years. I posted pics of my bowel inflammation back in 2012 which would scare the crap out of you (I will try to find the thread containing those pics and link it here). That was a low point before biologics. What happened since then is very effective treatment. But even then I was functional and not in awful shape. Anyway good luck-


Yea, I can see the inflamed pouch ! Thanks for sharing the pic.
Did you have to go on biologic immediately or few years down the line when pouchitis wont go away ? If you don't mind me asking, which biologic are you taking ?  
I am so glad, you found what works for you  and have good quality of life.

If not for side effects, I would not be so hesitant to biologics.  But, in general, I have observed, I am prone to side effects .
I am hoping I find the right treatment soon.
Also, yes, I agree that stool test wont necessarily tell enough. I also feel like are so many stool tests necessary? Maybe stool culture might help but not sure about noro virus, rotavirus. Dont they usually run there course and are out of the system maybe less than a week ?
( not sure for jpouch people )

But, since He is the doctor and its first time I am seeing him I feel he might get pissed off If I ask about the test. 😐  

Thanks a lot for your reply

Last edited by meghspd

The best way to answer your question is to give you a timeline on my IBD treatment as follows:

1972- diagnosed with UC at age 9

1992- after 20 years of deteriorating UC treated with prednisone and azulfidine (biologics did not exist in 1992) diagnosed with dysplasia of colon. Colectomy and J Pouch

1995- begin treating pouchitis with rotating antibiotics (cipro, flagyl, 4-5 others)

1995-2008 on antibiotics which only kept pouchitis in a "simmering" state; gradual increase in inflammation.

2008- inflammation observed in lower ileum and at J Pouch inlet; Crohn's Disease suspected

2009-2015 myriad diagnostic testing to determine Crohn's vs pouchitis and level of bowel wall inflammation; backsplash stool suspected to be playing role in inflammation of neoterminal ileum

2015-2019- Remicade plus antibiotics achieve total remission of pouch inflammation but not neoterminal ileum and inlet inflammation, GI calls this area "stubborn" and "treatment resistant"

2019-2021: Remicade only, no antibiotics

2021-2023: Remicade with antibiotics used only as needed when I get "runny", usually towards end of Remicade cycle but sometimes not.

2023: now 60 years old and a 51 year veteran of battles with IBD, although nobody has awarded me any medals for my service. Feel great. Still working full time as an attorney.

Last edited by CTBarrister


Thank you for the detailed timeline. It really helps understand the progression of the disease and somewhat will help me prepare for the future line of treatments.
I am 42 years and I hope I can manage the symptoms and am able to travel, eat and have some fun.
You are really a warrior and have been through so much. Kudos to you !
I wish you continued success with your treatment and life!

Had an Ilial-pouch-anastamosis (S-poouch) more then 30 years ago after UC that did not respond to anything except large doses of Prednisone.

Things were goo until about a year ago when I started having to go too many times during the night, as well as during the day.  New Gastro Dr. did a scope and said I either have inflammation int he pouch and into the small intestines.  He didn't label it Crohn's but rather IBD.  The look of the cells and a biopsy can tell them some of what to label the disease as.  With the new biologics I am not sure it matters.

We tried Remicade but it didn't work, I built up antibodies and no trace in my blood stream.

I am now trying Entyvio a different type of biologic.  Too soon to tell if it will help.

I had a bad case of runny stool in February where I lost about 6-7 lbs during the night, all fluid.  It was probably Noro or some other intestinal virus.  From that came a couple of kidney stones.  Dr. said if that happens again, go to emergency and get fluids.  I baby sits three young granddaughters and probably caught it from them.

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