I've had my pouch since 2000.  I also have had recurrent pouchitis throughout the last 16 years.  For that reason, I was put on Flagyl and Cipro, long term.  I tolerated both well until getting peripheral neuropathy in my feet and hands about 2 years ago and Flagyl was stopped.  I was then solely on Cipro for pouchitis and entocort.  This year, I became quite ill from C Diff and Cipro was stopped.  I tried several other drugs to no avail until my second round of Difficid.  Shortly after the C diff was gone, I became sick again w Pouchitis, as I was not on any antibiotics at that time.  I was again put on Cipro for a two week course which seemed to clear up the pouchitis.  Two weeks or less, I had pouchitis again.  I was put on Cipro for long term preventative of pouchitis.  My gut is fine now and has been for a month or two, however, my joint and muscle pain etc has gotten worse and worse to the point that my knees can no longer support me even lowering myself to the toilet, my hands are so painful that it is hard to do just simple tasks, my feet and ankles hurt with every step, as if (particularly when I get up in the am or middle of the night) I am walking on broken bones.  I have been to the rheumatologist and my blood work is negative for RA.  Though my hands and knees are swollen, he still didn't think I have RA.  

A few nights ago I told my husband that I could not keep living like this.  That night, I had an "ah ha" moment and wondered if any of my agonizing symptoms were Cipro related.  My GI doc had said that the only thing to watch for is pain in my Achilles' tendon because there is a very rare chance of rupture.  When I heard this a few months ago, I said, "well, I have been on Cipro for so many years and haven't had any adverse reactions, I'll be fine".  I had forgotten about what he said until the other night when it occurred to me that maybe it is not just the Achilles' tendon and I did some in the middle of the night research.  Much to my great surprise, there was a lot of information on the same symptoms of "hurting from head to toe" related to being on Cipro.  In the past, when I had been on Cipro, most of the time I also had pouchitis, so my doctor and I always assumed that my joints were hurting because of the gut inflammation (enteropathic arthropathy), and the other times, my doc would tell me that one can have the systemic enteropathic arthritis even when the gut or pouch is not inflamed.  I NEVER EVER thought of Cipro being a culprit, and historically after getting off of the Cipro, eventually my joints would get better and at that point, My pouchitis was absent.  The other night when  I heard my new GI doc's ( my old GI retiring after having been with him for 27 years!) voice whispering about Achilles' tendon rupture, was the first time I had EVER considered Cipro as the cause of this progressive musculoskeletal pain.

 I stopped Cipro two days ago and will remain off of it.  However, as my primary doc said "you NEED to find another medicine that you can be on to prevent pouchitis, in place of the Cipro".  That is what I need to know.  My current GI doc said that he didn't know of the best antibiotic to use but that he would "investigate".  That doesn't give me a lot of faith.  I have more faith in what you all have used and the success rate, of an antibiotic other than Cipro or Flagyl that I can be on that won't have these debilitating side effects.  That being said, I am not certain yet that the Cipro is responsible for the joint, muscle, tendon pain.  It is just my theory at this point, because nothing else makes sense!  Out of the blue, these symptoms again show up?  I am just praying that the symptoms will go away, as they have done before.

PLEASE let me know 1) if you have ever had this type of adverse effect from Cipro 2) what antibiotic have yo used to replace Cipro.

Thank you all so much.  I apologize for the lengthy entry/post.

Original Post

There are a fair number of other antibiotics used for pouchitis. If I were in your situation I'd try Xifaxan (rifaximin) next  - make sure your doctor doesn't use the low dose that's recommended for traveler's diarrhea. Xifaxan is very expensive, though. Other choices include Tindamax, Augmentin, and a few others. Good luck!

I've had my jpouch since 2001 and have had pouchitis on and off ever since. But I've used flagyl suppositories to keep it in check for at least 13 years.  there are zero side effects since very little is absorbed into the blood stream unlike oral medications.  They work almost instantly, a few days at most.  I just had a scope and my doctor was amazed at how there was no inflammation.  I would highly recommend the suppository route if concerned about antibiotic reactions.  

I am getting good results with Remicade and have been off antibiotics for over six months. Antibiotics are not the only treatment for pouchitis.


I do have quite a bit of Achilles pain in my left Achilles. I've brought it up with my doctors but they never seem to take it very seriously. This has been for a few years now.

I have an appointment coming up with my new GI in the next month and I'll bring it up again.  This guy has been great and is working with me on some things to try other than just take Cipro forever (which I have been doing since 2007 - 10 years now). I've been taking Lialda recently along with Cipro, so I'm hoping to try going back to Xifaxan along with the Lialda and cycle off Cipro if possible soon. We'll see. In the past if I go off Cipro I am non-functional within days.


Last edited by DJ H

Augumentin and xifaxin work great. Also I have psoriatic arthritis and developed it about 5 years after my JPouch. My bloodwork came back negative too, but the inflammation I was having in my joints was clear it was arthritis. I eventually had to go on Enbrel which worked beautifully. You need to explore options bc severe joint pain is awful and can be prevented with treatment. Good luck! 

Thanks so much everyone for your responses.  Could anyone tell me the dose of Xifaxin?  It was mentioned that I should make sure that it is the correct dose for pouchitis and not for "traveler's diarrhea ".  Thanks again all and a Happy and Healthy New Year!,,

Yes, three times in 2016... Each time with pouchitis.  Think I might try Xifaxin as this is one that many members have talked about.  Also considering Augmentin.  Don't know if one is easier than the other to tolerate?  Thank you so much for the dosing info!

Xifaxan is better tolerated than most other antibiotics, because the systemic absorption is minimal. I just hope you have good insurance, because it's quite pricey. 

I've had the same effects from cipro... and if you get them the side effects come faster.  When discussing them with medical professionals it seems 50-50... some will say "oh it's the flagyl" while others say "oh it's the cipro".  Has anyone got an idea or been tested to see which one it is?  I would try one or the other to see while I'm looking for an alternative but not both again.  

Has anybody else tried remicade or any other medication that's used to treat uc or crohns for pouchitis? If you have how effective was it ?

Marcus, there's no test (other than trying them separately) to tell which one is causing trouble. That's why I get so angry at doctors that prescribe both when only one is probably needed.

Tracy Bug thanks for posting on this. You've put the puzzle together with a re-exposure, as did I.

MUCH more awareness is needed amongst us Jpouchers who can be prescribed a lot of flouroquinolones and therefore represent a higher risk group for experiencing these awful adverse effects aka FQAD or 'flouroquinolone associated disability'. sadly, when we start getting any of these well documented side effects, they are usually attributed to an autoimmune/ IBD type cause and not the medications, which the FDA now finally acknowledges can cause disability due to the severity and long term nature of side effects. Based on anecdotal reports, it seems most doctors do not seem to recognise these side effects and they extend way beyond Achilles pain...

The fact is, that even extremely healthy people are taking even very short courses of these drugs for minor issues all over the world and many are reporting becoming partially or completely disabled. There are tens of thousands of them online supporting each other on various sites, if you look up on google or Facebook ' flouroquinolone toxicity' you will find them.  

Here are some links for your interest. Plenty of peer reviewed studies in the floxie hope link.







Please feel free to get in touch, would be happy to connect with you.

best of luck recovering and getting on top of pouch issues, agree rifaximin may be good and a lot safer. All quinolones, flouroquinolones you may want to steer clear of the whole classes of them to be on safe side


Last edited by claire

I alternated Xifaxan and Augmenten for 8 months straight and they didn't work. I can't take Cipro because, like you, it caused c.diff when I had my colon. I had it also in my j-pouch and was told never to take cipro again. I had to go off Flagyl because it made my perpherial neuropathy worse.  I also took Augmenten pretty steady before going to 100% on antibiotics.

I now have an ileostomy and my j-pouch was removed. So mine is not a success story. I feel much better without my j-pouch.  The ileo is better than my awful temp iLeo was. That said my j-pouch got sick within the first year and it was removed 5+ years after it was created. You had a healthy one for a long time. It would be great if you could get back to a healthy one so hopefully our suggestions help.

Last edited by TE Marie

I currently have had pouchitis since mid-Sept. It is the first time I have had it and I have had my j-pouch for 5 years. My doctor is treating it with tetracycline 500 mg 2xs daily and Entergam food supplement medicine and VSL 3. I am also on the Low-FODMAP diet. I feel these things are helping and I am improving. I have adverse reactions to Cipro and am allergic to Flaggl, so we had to go a different route. Best of luck to you!

Last edited by JenB

 Thank you everyone again for your responses and support. I have an appointment to go to see Dr. Shen  at the Cleveland clinic on February 7. I am hopeful that he doesn't react dismissively to my theory that all of this musculoskeletal pain is related to Cipro. 

 Claire, thank you so much for sharing the links. I have done a lot of reading but some of these are new to me. 

 So far three days on Augmentin has done nothing for my pouchitis. Sadly, I know that I have responded in the past very quickly to Cipro but since that is no longer an option, I will have to give this a longer try. If it still doesn't help after a week, I will go to the more expensive option and try Xifaxan.

thank you again everyone.

All the best Tracy... it's a bad thing to go through and a lot of us have been there.  I hope you get relief soon.  

JenB, please let us know how your treatment progresses.  A lot of us are looking for other options to cipro/flagyl... especially if it results in less meds and more of a natural treatment.  All the best.


Tracy clindamycin might also cover both Cipro and flagyl it worked for me until I got off antibiotics onto immuno suppressants..

tumeric golden paste and CBD also might be worth looking into as natural treatments

Speaking of Xifaxan and the high cost, I was thinking that the generic was due out soon, but I just looked it up and it isn't until 2019.  Aaargggh, yet another super expensive med.


I received my J-pouch in 2005, had a reoccurring bouts of pouchitis and was always put on cipro and Flagyl.  My pouchitis seemed to come like clockwork every 6 months... after about 3 years I had awful side effects and could barely get out of bed.  My GI doctor took me off the cipro and put me on Levofloxacin....another dangerous antibiotic in the same family as cipro.  I stopped that too and started researching the effects of cipro on the body.  There is so much information out there and so many people that become debilitated because of these drugs. I still have pain in my joints, arthritis like symptoms that have been ruled out as arthritis and am convinced it is due to the cipro and Levofloxacin.  I have managed my pouchitis naturally for 3 years or so (knock on wood).  As soon as symptoms appear that even resemble pouchitis I change my diet and increase my probiotics.  I have been lucky not to have chronic issues.  


Last edited by WendyNemec

Thank you Wendy!  Yes, I just had to get off of Cipro.  Have tried Xifaxin, probiotics, Augmentin, but after 20 years on Flagyl, I had to stop that due to neuropathy.  I have truly run out of options. 

I would love to know how you have changed your diet and the kind and amount of probiotics you are using.  The VSL3 costs me $400/month and no /my insurance won't cover.  And you mentioned "treating it naturally"... any other suggestions? Thank you again and SO glad that you're doing well!!!




If you're going to spend the money on VSL anyway, it's likely worth *seriously* appealing the insurance denial. Your best bet is based on "medical necessity," and you'll almost certainly have to escalate the appeal to your state's insurance regulator. I was successful, but it took a year (and then some follow-up the following year). I even got reimbursed retroactively, but only because I asked for it.

Ok, well haven't been on here for a while. Tracy, recently (in last couple months) my doctor put me on Xifaxan 550 2xs a day and Dicyclomine 4xs a day. I also take VSL 3 probiotic twice a day and am still on the low-FODMAP diet, just recently with a nutritionist's help. This on top of eliminating some stress and getting some prayer(I believe this was the most important thing for me), and I'm finally getting better! I've had since mid-September. I wish you all the best. I hope this helps. I don't know anything about Cipro related arthritis like symptoms. But I definitely would recommend the Xifanan, and Dicyclomine. You'll be in my prayers too. Hang in there lady!

What I do first is cut out all sugar, change to a completely bland (and as soft as possible) diet, increase my yogurt intake (and lactaid intake!), and overall decrease my food intake for a few days.  I have never tried VSL's, but take a daily "Align" probiotic.   I have successfully managed pouchitis this way by immediately recognizing the onset and getting ahead of it.   Stopping sugar intake seems to be key for me, eating the extra yogurt helps with the good bacteria and the rest is to just give the pouch a break while I am fighting off the pouchitis.   It seems to be working for me so far, but I have learned that what works today may not work next year...and what I can eat today may cause me issues next time I eat it.  It's a complicated experience this Jpouch thing!

I hope you find what works for you!

I have never seen Alinia mentioned here but it is something I use when I have to go the the well when nothing else works.  It is an antibiotic that is used to kill Cryptosporidium.  All I know is that it works for me.  I take 500 mg a day until I better control of my inflammation.  My Doc prescribed it several years ago and he doesn't know why it works.

I would encourage anyone suffering with our issues to read "Grain Brain".  It covers a multitude of problems that occur foods that promote inflammation.  I have felt a lot better just going Paleo.  It might not be a cure but it sure helps with maintenance.  I agree, get rid of sugar completely.  You will find after a few months the craving for it will be gone.  You can always sweeten with some local raw honey if you need to.  Really pay attention to labels... everything is filled with it.. sugar, corn syrup, etc.  Good health everyone!

I have had good results with Remicade. I've been off antibiotics for a year now.

Remicade does not seem to work as well as other biologics for my arthritis, but maybe that was progressing anyway.


Been on everything, tried everything , Im on Entyvio now. You should look into the bio drugs. I was scared at first but my body needs them and I think the antibiotic messed my flora and made my pouch worse. 

Thank you everyone for your input.  Am trying out a new doc in OKC.  I've been on the Xifaxin for about 3 months now.  Though my stools are still liquid, the pain is a bit better but not gone.  After Dr Ali looks at my pouch, he'll give me his opinion re biologics.  He, like the last couple of docs, brought up the possibility of going to an ileostomy.  Just can't wrap my head around that yet.

Hello, Marcus1959. I also stopped using white sugar. I use raw, unpasteurized honey to sweeten my daily coffee, tea, toast. It seems to make a difference. I know sugar is sugar, but raw, unpasteurized honey is a natural product made only by honey bees. I get it from the health food store or Amazon. It has to be better than refined white sugar. 


I am glad you are doing better. If you ever want to ask questions about going to an ileostomy please PM me and/or look in the Ostomy section on here. Several of us went through the surgery and ileostomys at the same time around a year ago and had discussions about issues with that. It isn't fun but I am feeling much better.  

Franklat posted:

I've had my jpouch since 2001 and have had pouchitis on and off ever since. But I've used flagyl suppositories to keep it in check for at least 13 years.  there are zero side effects since very little is absorbed into the blood stream unlike oral medications.  They work almost instantly, a few days at most.  I just had a scope and my doctor was amazed at how there was no inflammation.  I would highly recommend the suppository route if concerned about antibiotic reactions.  

Franklat, where were you able to buy Flagyl suppositories? My GI doc, my Pharmacist and I have scoured the internet and not found any companies that make it. Even tried Canadian Pharmacies, no luck!

They tell me they are not made anymore, nor made by any compounding pharmacies. I'm located in Eastern PA, which may not be relevant in obtaining them? Any info would be appreciated? Thks!

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