• Welcome to Crohn's Forum, a support group for people with all forms of IBD. While this community is not a substitute for doctor's advice and we cannot treat or diagnose, we find being able to communicate with others who have IBD is invaluable as we navigate our struggles and celebrate our successes. We invite you to join us.

Anti-MAP Therapy Support Group

The Anti-MAP Therapy Support Group.

Some papers on the immunodeficiency hypothesis

Crohn's as an immune deficiency: from apparent paradox to evolving paradigm.

Disordered macrophage cytokine secretion underlies impaired acute inflammation and bacterial clearance in Crohn's disease

Revisiting Crohn's disease as a primary immunodeficiency of macrophages

Is Crohn’s disease due to defective immunity?

Defective acute inflammation in Crohn's disease: a clinical investigation

Neutrophil Dysfunction In Crohn's Disease

Vitamin D, NOD2, autophagy and Crohn’s disease

Abnormalities in the handling of intracellular bacteria in Crohn's disease: a link between infectious etiology and host genetic susceptibility.

Crohn’s disease as an immunodeficiency

Defective innate immunity in inflammatory bowel disease: a Crohn's disease exclusivity?

Is Crohn's disease an immunodeficiency? A hypothesis suggesting possible early events in the pathogenesis of Crohn's disease.

Crohn's disease: an immune deficiency state.

Integrating theories of the etiology of Crohn's disease. On the etiology of Crohn's disease: questioning the hypotheses.

The immunopathogenesis of Crohn’s disease: a three-stage model

Mycobacteria in Crohn's disease: A persistent hypothesis

Mycobacteria in Crohn’s disease: how innate immune deficiency may result in chronic inflammation


Compiled literature and resources on the MAP hypothesis









Efficacy and Safety of Anti-MAP Therapy in Adult Crohn’s Disease (MAPUS).

Open Label Efficacy and Safety of Anti-MAP (Mycobacterium avium spp. paratuberculosis) Therapy in Adult Crohn’s Disease (MAPUS2).

RedHill Biopharma Accelerates RHB-104 Phase III Study in Crohn’s Disease with Top-Line Results Expected Mid-2018

Crohn's Map Vaccine




A Study to Determine the Safety and Immunogenicity of a Candidate MAP Vaccine ChAdOx2 HAV in Healthy Adult Volunteers

---------- / ----------

2017 MAP Conference Presentations

The Consensus from the Mycobacterium avium ssp. paratuberculosis (MAP) Conference 2017

Anti MAP Forums and Groups

Human Paratuberculosis Foundation Facebook Group


Patient Stories

Patient Information Leaflet: Anti-MAP antibiotic therapy for the treatment of Crohn’s Disease

Treatment of Crohn’s Disease using Anti-MAP (AMAT) Therapy

AMAT questions answered by Dr. William M. Chamberlin

MAP Specialists

MAP Doctors and Research Centers Around the Globe

MAP diagnostic test by Otakaro Pathways


Videos on Youtube

Crohn's: autoimmune or infectious disease? Public presentation by Marcel Behr.

Prof Borody; Crohn's Interview - Part 1 of 9

Part 1-CROHN M.A.P. by John Hermon Taylor

Patients' stories
Last edited:
Macrolides and other antibiotics may cause serious neurological and psychiatric side effects in some people.

The mechanisms involved in macrolide induced psychiatric reactions
are not well established. Several theories have been proposed:
1) drug interactions due to the inhibition of cytochrome
P450 by clarithromycin; 2) accumulation of the active metabolite
14-OH of clarithromycin in the central nervous system; 3)
increased levels of blood cortisol and prostaglandins, hormones
that are associated with mania (6,10,11).
Psychiatric adverse reaction induced by Clarithromycin

Pharmacovigilance data collected from several European countries show that macrolides can provoke neuropsychological adverse effects such as hallucinations, delirium, manic episodes and sometimes depression, in both adults and children. These effects seem to be rare and are reversible on macrolide withdrawal.
Neuropsychological effects of macrolides

In the literature, different forms of clinical
symptoms have been described as consequences
of the effect of macrolide antibiotics on the CNS
(mania, psychotic reaction, delirium, nightmares,
psychomotor agitation)6-11. In 1981, Cohen and
Weitz first described two cases of psychiatric
complications in patients who received
erythromycin12. The exact mechanism of the
described side effects is not known. There are
numerous assumptions and explanations that the
active metabolite of erythromycin passes through
the blood-brain barrier and causes imbalance
between GABA-ergic and glutamatergic activities
in favor of the latter13. The literature also mentions
the possible antagonization of GABA A receptors,
protein and pyridoxine synthesis inhibition14, and
an increase in endogenous glucocorticoids in the
CNS15. Thus, in the face of various assumptions,
the mechanism remains unknown. We must bear
in mind that erythromycin is one of the important
inhibitors of cytochromal enzymes in the liver,
possibly also affecting the pharmacokinetics of
other drugs in the body.
Erythromycin-Induced Psychotic Decompensation in a
Patient Affected by Paranoid Schizophrenic Psychosis

The principal side effects of clarithromycin are gastrointestinal; however, less commonly, CNS side effects have been reported, including dizziness, vertigo, anxiety, insomnia, tinnitus, confusion, disorientation, hallucinations, psychosis, and depersonalisation.1 At the time of writing the Committee on Safety of Medicines (CSM)/Medicines Control Agency (MCA) have received 219 reports of suspected clarithromycin induced psychiatric disorders including psychosis (n=5), depersonalisation (n=5), and suicidal ideation (n=4) (CSM, personal communication). It has been postulated that macrolide antibiotics may cause a psychosis-like syndrome via their inhibitory action on glutamatergic neurotransmission in the brain.2 Nevirapine has not been reported to cause serious CNS adverse effects.3
Neuropsychiatric reaction induced by clarithromycin in a patient on highly active antiretroviral therapy (HAART)

We reported two cases of end-stage renal disease (ESRD) patients who developed hallucinations such as vivid images of worms after taking clarithromycin. Similar to previous case reports of clarithromycin neurotoxicity, the visual hallucination resolved upon cessation of clarithromycin.
Clinical manifestation of macrolide antibiotic toxicity in CKD and dialysis patients

Although the psychotropic effects of antibiotics are not commonly utilized therapeutically, the commonly associated side effects confirm their potential to influence CNS function. Several antibiotic medications have been known to cause confusion, anxiety and depression and in some instances, psychosis [13]. Although unfavorable in a therapeutic context, these effects are often influenced by age, dosage, blood–brain barrier (BBB) permeability and drug interactions. Research into the mechanisms behind these effects may help to elucidate a therapeutic application. Penicillin for example was known to act on GABA receptors, a mechanism thought to be responsible for many of the side effects [14]. Other classes of antimicrobial compounds, particularly the antimalaria treatment methylene blue and several antituberculosis drugs, have been shown to have monoamine oxidase (MAO) inhibitor (MAOI) properties.
Psychotropic effects of antimicrobials and immune modulation by psychotropics: implications for neuroimmune disorders

Nervous System Effects of Antituberculosis Therapy

Adverse effects of macrolide antibacterials.

Penetration of Drugs through the Blood-Cerebrospinal Fluid/Blood-Brain Barrier for Treatment of Central Nervous System Infections†

Nervous system effects of antituberculosis therapy.

Neurological manifestations and toxicities of the antituberculosis drugs. A review.

[Adverse effects of antitubercular drugs: epidemiology, mechanisms, and patient management].

Adverse Effects of Macrolide Antibacterials
Other possible side effects that I remember:

Fatigue, nausea, headaches, bad taste in mouth, dizziness, brain fog, reduced apetite, diarrhea, joint pain, oral candidiasis, c. diff. infection, cardiac arrythmia and hepatoxicity, tendon rupture (Cipro), bacterial resistance to antibiotics.
Last edited:

Deleted member 431298

Another anecdotal case report of long-term remission induced by anti-MAP treatment.

Dr. Lipton struggled with IBD from 1986 until 2004. She had multiple flares, sometimes called Ulcerative Colitis, but finally Crohn’s. One day, as she was resting in bed recovering from a flare that landed her in the hospital, she read a medical magazine and came across an article about a microbial agent, Mycobacterium Avium Paratuberculosis (MAP), and its potential connection to Crohn’s disease in humans.
On 12/10/04 Dr. Lipton began a special antibiotics regimen guided by Dr. Borody. She responded to the treatment well, all her Crohn’s symptoms vanished. She spent 5 years on the antibiotics, ensuring that all the harmful MAP bacteria were eradicated. She decided to stop the antibiotics treatment in 2010, feeling that this allowed plenty of time to assure her sustained wellness. These days, Dr. Lipton continues to be in complete and total remission, without any special diet and without any maintenance medications.
Another anecdotal case report of long-term remission induced by anti-MAP treatment.

Dr. Lipton struggled with IBD from 1986 until 2004. She had multiple flares, sometimes called Ulcerative Colitis, but finally Crohn’s. One day, as she was resting in bed recovering from a flare that landed her in the hospital, she read a medical magazine and came across an article about a microbial agent, Mycobacterium Avium Paratuberculosis (MAP), and its potential connection to Crohn’s disease in humans.
On 12/10/04 Dr. Lipton began a special antibiotics regimen guided by Dr. Borody. She responded to the treatment well, all her Crohn’s symptoms vanished. She spent 5 years on the antibiotics, ensuring that all the harmful MAP bacteria were eradicated. She decided to stop the antibiotics treatment in 2010, feeling that this allowed plenty of time to assure her sustained wellness. These days, Dr. Lipton continues to be in complete and total remission, without any special diet and without any maintenance medications.
An earlier post from Dr. Lipton:


The comments section has some information too.

Deleted member 431298

Recently uploaded to YouTube:
a five minutes long profile of Dr. Thomas Borody, who is one of the practitioners administering Anti-MAP therapy from his clinic in Sydney, Australia.
He is one of the few doctors to openly state that he firmly believes CD to be an infectious disease.
Dr. Borody was also behind the development of the triple antibiotics therapy for gastric ulcers, which target the underlying infection by the H. Pylori bacteria.
The treatment is now considered the gold standard for gastric ulcers.

PS. Thank you! Crohn2357 for posting the link to Dr. Lipton's blog page. You are right, both the blog and the comments are an interesting read!
Last edited by a moderator:
Hi guys, have you been donating for the anti-map vaccine?

have you been on some anti map therapy?
Last edited by a moderator:

Deleted member 431298

Hi Guerrero.
No, to be honest I have not yet donated to the vaccine development. I know I ought to. I did support John Aitken's lab by ordering a MAP blood culture test.
Did you donate?
Also, I have not tried anti-MAP therapy. I am monitoring the news from Redhill about their phase III study, and I am in an almost daily debate with myself whether I should try to find a GI that will prescribe the drugs or not. It's just that no doctor I have ever spoke to seems to think MAP could be causing CD. Also, none have shown real interest in the research. So I would probably have to look abroad (to the UK) and that is just a bit of a mouthful to do.

It would be very interesting to hear from someone currently on the antibiotics!
Ole - I'm on AMAT and it has changed my life. The antibiotics do work for some people. I have inflammatory markers and colonoscopy results from before and after AMAT. Horrible before, felt like I was pretty close to being hospitalized and barely able to leave my house, to no trace of Crohn's even three years later. The docs call me a miracle responder. After 25 years of this horrible disease, it's like I never had it. My mucosa is healed, and I feel great. Never thought it would happen. So at least for some people, it works. Sometimes it's not as dramatic, but a fair amount reach remission. At least as good as other therapies in my opinion.
Also Ole - have you seen HumanPara.org? There are other patient stories on there and since I talked to the people and put their stories on the site myself, I know for sure these are real people who have had their life changed by AMAT. It's interesting to see the variety of response to AMAT. Some were quick like me, others took a longer time. I know for some, it doesn't work or they cna't tolerate the meds. Look under the Crohn's tab. I also think RedHill will be very successful. Just waiting for the final data. We're getting close!

Deleted member 431298

Thanks, Irisgal for the useful and relevant info. Congratulations with being in complete remission without any of the usual heavy immunosuppresant drugs. That is truly amazing.

I have been in remission on Methotrexate, and five month ago I sent blood to John Aitken's lab and they found viable MAP in my blood. Very low numbers, though, consistent with a patient in remission (which I was at the time). As an experiment, I have tried to quit dairy/beef and taper the MTX.. could it be that avoiding re-exposure to MAP alone would keep me in remission?
Sadly the answer seems to be no. Six weeks without MTX now and the CD symptoms have returned over the last two weeks.
I will now send another blood sample to Aitken, to see if more viable MAP can be found. I hope that can assist the decition whether to try to get on AMAP or not.

Although I have been visiting humanpara.org alot, I had not noticed the patient stories. I am going to read through them with interest.
Sorry you are flaring Ole. I think it's a lot more than MAP ingestion once the disease triggers. It's trying to control the whole immune cascade. Will be interesting wha your current sample will show as compared to the last one. And I definitely tried all of the conventoinal therapies first (minues 6MP and MTX) but nothing worked. AMAT wasn't so much of a choice as it was the only viable thing left! But I'm glad I did it. Trying to figure out an end game as I've been on for 3 years now. Let me know how you do!

Deleted member 431298

Thanks, will do :).
Trying to figure out an end game as I've been on for 3 years now.
I take it you already studied Dr. Lipton's case? An article about her reads:
She spent 5 years on the antibiotics, ensuring that all the harmful MAP bacteria were eradicated (this kind of bacteria is a very slow propagator, so the working assumption is that it takes a long time to ensure all traces are eliminated). She decided to stop the antibiotics treatment in 2010, feeling that this allowed plenty of time to assure her sustained wellness.

Yes - I've spoken with Dr. Lipton, but I think back then the thought was that you could erradicate it completely. In my long term case, I don't think that's going to be possible, and I'll still be genetically susceptible. My goal is to keep the little I have left in dormancy.

Deleted member 431298

Update on my getting-to-know-my-MAP-levels-trend quest:

I Fedex'ed two blood samples yesterday. Quite the logistic puzzle, but I'll spare you the details. I emailed the lab, briefly explaining my situation: That I had another test done five month back, positive but with low numbers of MAP (I was in remission at the time). Then, how I had tapered Methotrexate and stopped altogether two month ago, and was now in a (mild) flare.
John Aitken himself replied, and took the time to explain a few things (I am really impressed he did):

He said they see a gradual reduction of plasma levels of MAP in the first six month after AMAT treatment is started, but that it takes alot longer to clear the organisms inside the macrophages.
He also explained that it is the extracellular MAP that cause inflammation, by producing biofilm. Biofilm production is hindered inside the cells. Anti-MAP therapies, he said, reach the extracellular bacteria first because are an easy target. The drugs prevent them from forming biofilm, thus giving a theraptutic effect. The intercellular ones are harder to get.
It seems no matter how long MAP is targeted by antibiotics, some mycobacteria manage to survive. So basically for the last bit he echoes what you write, Irishgirl, that the goal (at the moment) must be to limit the infection to a point where the mycobacteria can not form biofilm (dormancy).

What a bummer that appearently AMAT is not able to clear the MAP infection completely.
Maybe then the Crohns MAP Vaccine is our best bet in the long run, and the antibiotics to be seen as a bridge therapy until JHT and his team hopefully completes stage III with success.

Irishgirl - if AMAT is no longer an option, what other options are you considering?
Could a low dose MTX maybe work? I seem to be in remission on 7.5 - 10 mg / week. Then again- the reason I investigate this is I really want to get off MTX, because of the side effects (nausea, anemia, cancer risk).
Or why not just stay on AMAT? Are you experiencing side effects?

By the way, your story, and the patient stories at HumanPara are really encouraging. I understand you have been a part of making human para, congratulations on a job well done.
Last edited by a moderator:
Traditional therapies, he said, reach the extracellular bacteria which are an easy target. The drugs prevent them from forming biofilm, thus giving a theraptutic effect.
What do you mean by "traditional therapies" and "the drugs"?

I've used mtx injections three years ago. It's a nasty drug; but if it keeps you in remission with a dosage of 7.5 - 10 mg/week, then I think it is not a bad deal. It can save you some time until the Redhill study publishes its results.
Cytotoxicity of macrolide antibiotics

Influence on Mitochondria and Cytotoxicity of Different Antibiotics Administered in High Concentrations on Primary Human Osteoblasts and Cell Lines▿

Cytotoxicity of macrolide antibiotics in a cultured human liver cell line.

Macrolide Antibiotics Exhibit Cytotoxic Effect under Amino Acid-Depleted Culture Condition by Blocking Autophagy Flux in Head and Neck Squamous Cell Carcinoma Cell Lines

Mechanisms of Action and Clinical Application of Macrolides as Immunomodulatory Medications

Deleted member 431298

A) What do you mean by "traditional therapies" and "the drugs"?

B) I've used mtx injections three years ago. It's a nasty drug; but if it keeps you in remission with a dosage of 7.5 - 10 mg/week, then I think it is not a bad deal. It can save you some time until the Redhill study publishes its results.
ad A). both should have referred to anti-MAP therapy. I corrected it in the post.
ad B). my thinking too. I try to look to the next therapy, though, because I have learned the hard way immunosuppressants can fail. I had a really bad kidney infection, likely from anti-TNFa drugs. Those drugs being the only thing doctors suggest, AMAT is probably the only option left for med if MTX fails to work or if I get another opportunistic infection.
What drug(s) are you currently taking, if I may ask?

Re. your links to cytotoxicity of macrolides, can you explain a little more about what that means: what happens if one gets such a reaction, what are the symptoms, and will it reverse if you quit the drugs?

Do you know if rifabutin and clofazimine are also considered macrolides, or it it only clarithomyzin?

Also, do you know if such reactions have been reported with AMAT therapy (such as in the Selby study)?
OleJ - I've been on AMAT full strength for nearly 3 years, and started getting a slight bit of joint pain which I couldn't determine if it was from the antibiotics or if it was the CD breaking through. My version of CD seems to break through therapies quickly (Remi only made it 6 months) and I ran out of anything approved, so went to AMAT. I was lucky thta stopped it cold, but I'm under no illusion that eventually the disease will figure a way around even AMAT. The only way to puzzle out the joint pain was to stop AMAT - a scary prospect after 3 years of being better!

I talked to my docs, and they all thought it was safe to pulse one week on, one off. Last week I stopped the antibiotics completely, promptly caught my husband's upper respiratory infection, and was miserable all week, but no GI pain, no CD symptoms, and the joint pain almost entirely went away. So it looks to be the meds giving me joint issues, and I wonder if that will continue with the every other week system. I had both CD caused joint pain prior to AMAT, and also bad joint issues when I was on levofloxicin as part of AMAT. I dropped the levo, and am only on clarithro and rifampin now, plus low dose naltrexone. I also daded some supplements, including a spore forming probiotic called MegaSporeBiotic and have started 8 hour intermittant fasting. I'm back on AMAT full strength as of today for a week. We'll see how it goes,but I'm hoping this could be a nice compromise to keep my dormant MAP in check while also minimizing AMAT side effects. Other than the joint pain now and the initial flu-like symptoms, I have had no other side effects on AMAT.

It's all about balance, and buying time for me. I think some cool therapies will be coming. RedHill is a great option, plus Qu with their SSI looks interesting. If we could get the Dietzia and EpiBro research going, they may pan out as well. Plus, there's a lot of dietary and natural options being looked into that could support immune health. I doubt I'd ever try MTX. It would feel like going backwards to me. I don't think the immunosuppressants are very effective, and am nervous about the side effects of that one in particular. A course of prednisone is what I may fall back to if needed.

Glad you like Human Para. I try. I just wnat to provide the resources for people that I had to hunt so hard for initially, and it's ballooned into a platform for all sorts of different research groups around the world. Many positive things coming out of that effort, and it's a great team. Hoping to start funding research VERY soon. Lots of legal junk to wade through in running a non-profit, but the MAP and other pathogenic research is the most promising stuff I see out there for CD, along with therapies that will rehab the broken immune system. We'll kick CD eventually! I'd rather it be sooner than later.

Let me know how you do with your testing. :)
OleJ, I am on 6mp.

Keep in mind that I have no medical training; I am researching this stuff because I may use the anti-MAP antibiotics in the near future. I wouldn't mind the short term effects of the antibiotics because in that case the benefits generally outweigh the risks; but I am not sure how the antibiotics would affect me in the long term.

Different cytotoxic agents may exert cytotoxicity through different mechanisms.

The side effects depend on the dosage and the individual. They don't have to be acute reactions, just taking a drug that has cytotoxic effects is problematic on its own. Again, I wouldn't mind it on a short period of time, like we use them to treat common infections; but how these affect you in the long term is what I wonder. Because, AFAIK, there aren't a great knowledge on the long term effects of these.

Clarithromycin is a macrolide antibiotic. The other two are part of the drugs called antimycobacterials.

I haven't read the full text of the Selby study, so I do not know the details of it.

Deleted member 431298

Crohn2357: Thanks for clearing that up. I have no medical training either, and ultimately I would leave decisions such as therapeautic effects vs. side effects to the GI, should I go forward and try to get on AMAT. At least you tolerate 6MP, that's a good thing. (I didn't).

Irishgirl: Thanks for the honest update. I really hope the weekly on/off cycle will give you both pain relief and remission. Let us know how you do. Yeah, it seems something in CD research is about to pay off. Now it's on to reading about the Dietzia and EpiBro research you mention, both are new words to me :)
Hi everyone, I'm new here, but not new to this subject. I was asked to join this forum so I could post my MAP story here.

I have ulcerative colitis, not crohn's, so my experience may or may not be relevant to others. My UC has been refractory to all modern drugs. The only other drug I am taking that has good result is Low Dose Naltrexone. My GI doctor has me on Entyvio and it only sort of works. If AMAT helps me more, I will stop Entyvio because its long-term side effects are gnarly.

MAP was identified in my blood by blood culture in August 2017. I will be starting the AMAT protocol on November 1st 2017, consisting of: clarithromycin 250mg TID, rifampin 300mg BID, clofazimine 100mg QID

All of the scare research in this thread about the effects of the antibiotics are kind of inappropriate, in my opinion. If you look at the list of side effects of all the commonly accepted IBD drugs, the list is very large. Treating IBD in general carries some danger, but the disease is worse. I would rather risk side effects than have my bowel removed.

Most of the macrolide side effects are dependent on your individual metabolism. If you tend to do poorly on modern drugs in general, then you are more likely going to experience intolerance symptoms. The other issue is the modern research does not adequately differentiate between true intolerance and die off symptoms. A lot of people really suffer in the first 3 days - 1 month of AMAT therapy and it's because their body's flora are going through massive shifts in the presence of these antibiotics, not to mention the primary pathogen itself dying off. If you have no other maintenance protocols in your life like diet, probiotics, herbal medicines, etc... then you will probably suffer more. I would not do AMAT on its own with no other support.

You can titrate your dosages upwards, starting at a small dose, or you can start at full dose. The former is usually recommended. If titrating and giving it some time does not lead to improvement, then these medicines may not be for you.

The rare side effects stated in this thread almost never happen, and are usually accompanied by other effects first. If you have any body awareness whatsoever you're going to abandon ship before something crazy happens. You can do all the scary research you want and take it into account, but at some point you're going to have to accept the unknown and try the meds if you want to have a hope of getting better.

I refuse to let them to take my bowel just because they are too ignorant to really treat this disease. I won't do it. I respect other people's choices so don't take it personally. But I have witnessed so much terrible incompetence in the treatment of IBD that I can hardly endure another moment of it. Maybe I just live in a bad part of the world for treating IBD, but it is worth finding an alternative cure just to get away from these sociopaths.

My GI wants nothing to do with the AMAT protocol. Luckily I have an understanding GP who will do it for me. Even so, I am basically doing a self-directed treatment here because the medical system is totally oblivious to the work of Borody and Chamberlin. All my main supports come from the AMAT community online. There are a few doctors in the world who can give us some guiding advice, but we are really on our own. We don't need to see hundreds of scary research studies on macrolides, thank you. We are pioneers in IBD treatment -- we know that we're off the grid and that you don't support us. But nothing will stop me from trying this, nothing. I have a proven infectious disease in my body and the fact that modern doctors won't look at it is, to me, a cardinal sin. I want it out of me.

The more people who try this and get better, the more we can finally start helping people. Colostomies and resections can be a thing of the past. It seems like every major breakthrough in the way we approach disease comes from outsiders who were shunned but took the risk anyway.

Deleted member 431298

Thank you for joining Conner, and for sharing your story, your thoughts, and your research.
It's a good point that the list of side effect alone should not necessarily disqualify trying AMAT, but at least for my part being followed by someone who knows what he/she is doing would definately be reassuring if I am to start. As you write, it is a matter of personal preference. To be fair, I don't think it is Crohn2357's agenda to do scare us all, my guess is he just wants as much as possible on the table.

I second your observation on GI's. For a year I have tried to get my GI to at least read the re-analysis of the Selby study, and see the informative lecture from Dr. Behr, but he never did it. He did agree to confer with GI colleagues at another hospital regarding my positive MAP test. Only I never heard from him, and when I went to the hospital to have blood drawn for another test, the GI nurse told me he has quit. So at the moment I am without a GI, with the prospect of getting a new one who most likely has not read any of the recent publications on the link between IBD and MAP.

For those of us who are seriously considering AMAT, updates on how you do going forward will be appriciated. Lastly, I could imagine there are UC patients out there who would also be interested to hear if this can have an effect given your diagnosis.
I was going to post a link to a study about MAP and UC but I can't post it until I've made 10 posts or more. Weird policy, but OK.

I've heard from some AMAT doctors and Crohn's patients that UC is caused by something else and that MAP theory is not the focus. But then I have come across UC patients who have used AMAT to achieve remission, and I have read studies like the one I was about to post that link MAP to UC.

Bottom line... there is MAP in my system and my UC is not responding to treatment, so I might as well try this. It's suspected that UC patients were infected later in life or with a smaller concentration, whereas Crohn's patients had a higher loading dose of mycobacteria or they were infected as children.

My blood culture shows my MAP concentration is small compared to the Crohn's patients I've talked to. My body is very clean, I live a very organic lifestyle and I am sensitive to contamination across the board. It may be that even a small number of these organisms were enough to make my body flip out. I ate whatever I wanted and lead a normal life until I was 29 and then all hell broke loose. I spent 2 years living in Asia and got very sick many times there, so for me the infectious connection is obvious.

In cattle, young calves are infected by their mother's milk, but they don't develop Johne's disease (the cow equivalent of Crohn's) until adulthood, so there is a delayed reaction. Same as in humans. The main distinguishing features between human and cattle versions is that in cattle, we can find MAP in bowel biopsies but in humans it's not observable in the bowel tissue itself. It may be in our lymph tissue and blood instead, things that the bowel is rich in.

Either way, with a remission rate of higher than 50%, AMAT therapy is still proving to be better than all the crappy immunosupressive drugs they have us on. I guess AMAT therapy is not as profitable compared to the tens of thousands (sometimes hundreds of thousands) of dollars people spend on immune suppression for IBD every year.

The key factor is that MAP is everywhere. It's in water, soil and air. Everyone alive on planet earth comes into contact with it, but not usually in significant numbers, nor do they develop any kinds of symptoms. So there may be an immune deficiency component that allows us to get infected. I know for myself I was immune compromised the entire time I lived in Asia, with constant GI distress. It's possible that allowed MAP to take hold.
P.S. Sorry if I got a little short about the "danger" studies. I have been researching the ins and out of this topic for 6 months or so. I have a scientific background. Despite all this research, I still feel unprepared to start taking the medication. If more doctors were doing this, there would be more clinical experience to rely upon. Instead all I have to go on is research and the stories of other patients who have done AMAT.

At some point you have to take that leap of faith and dive into the unknown. All the research in the world can't tell you what your body is going to do, nor can it predict biological systems perfectly. Our knowledge of the body and disease is still very imperfect.

I take the plunge in just a few days. I will post my progress, though maybe not at first. The blow by blow might scare people. I expect at least the first week to not be very fun.
I agree Connor - it especially irks me when mpthe mainstream GI community dismisses the risks of biologics (like untreatable Tcell cancer!) but freaks out when I'm going to take antibiotics that have been used for decades in millions of patients. I think for normal people, with healthy gut flora, antibiotics can be VERY bad. I think we're only figuring out how bad thta is now, and even at low levels in food they are bad. But for CD (and maybe UC patients) our flora is junk. It's hurting us. So antibiotics give us relief and stop whatever is destroying us. It's hard to know exactly what role the microbiome plays alongside MAP. We just need more research to answer some of the critical questions, but as you mention, treating IBD is a risk analysis. Uncontrolled disease and inflammation is probably worse than the side effects of any treatment, and I wish the docs wouldn't get so comfortable with the biologics. It's like they've been brainwashed by BigPharma and it's been beaten into normalcy due to the pervasiveness of these treatments at seminars. Side effects have been minimized.

For me, I was sick with colds and viruses constantly while on biologics. The printed material on both Remi and Humira clearly state that's a big deal, and to tell your doc. I'd do that, and they'd just tell me I have a cold. It was no big deal. But I got multiple rounds of sinus infections and bronchitis. It didn't even phase them. I quit telling them. Plus, it did nothing for my CD. AMAT is absolutely a viable treatment, and I'm hoping RedHill will prove that once and for all. Good luck with your journey! I don't envy you those first few weeks.
If you think the only negative effect of antibiotics worth considering is their ability to manipulate your microbiome, then you need to read and think a lot.

“People almost invariably arrive at their beliefs not on the basis of proof but on the basis of what they find attractive.”
― Blaise Pascal

If you want to make a proper risk analysis, you need to study the risks.

Being reactive to questioning has always been a sign of stupidity. I have no motives to change yours, so I will not give any further replies to your comments.
Last edited:

Deleted member 431298

Six years ago, while on Humira, my creatinine levels suddently started to rise. A biopsy revealed chronic changes to both kidneys (interstitial nephritis). Could be an extraintestinal manifestation of CD, but most likely a side effect of the biologic, according to my specialist.
Better get off it, the GI said. So I did and got quite sick very quickly. OK, the GI said. Lets try Remicade. OK I said.
A year later, I was sitting the chair reading while the Remi was dripping through the IV i heard a "Thump" and the person next to me fell over in spasms. The nurses picked her up, tilted the chair backwards, stopped the IV and gave her an injection. Slowly she came to. She was taken to another room, the rest of us continued.
One year after that, creatinine started to rise again. Estimated kidney function now 40%. Then I stopped biologics for good. I have managed to do without, but that's another story.

My point is this: Bring ignorant about side effects is one thing, making a judgement call between risk of side effects and therapeutic benefit is another. I believe Conner is doing the latter.

Sure, the antibiotics could result in some unwanted cytotoxic reaction, but hey, we are already in a place where there are certain risks no matter what route we go, whether it be biologics, sterorids, AMAT, cancer drugs or nothing at all.
Crohn2357 - I assume your vitriol is directed at me? And now that I'm reacting (for the benefit of all on this thread) I guess I'm "stupid?"

I never mentioned that I believed microbiome shifts were the only negative effect of long term antibiotics. I don't know where you got that. My above comment was specifically questioning the effect of antibiotics on gut bacteria as related to the interplay of MAP. I know long term antibiotics can have significant side effects as you mentioned. But so can all other CD treatments, and when the patient is out of traditional options, most are willing to assume more risk since untreated CD presents a serious risk as well.

Not really sure why you started this thread if you are stressing the risks of antibiotics and not looking at the benefits as well. And no need to get nasty. This is an open dialogue between patients who are suffering and want to learn. I've been lucky that AMAT has healed me and I haven't had serious permanent side effects. To get a prescription, presumably every patient would have to discuss the risks and benefits of AMAT with their doc, and also be continuously monitored for side effects. Don't really see what your problem is, but seems as if you have an ax to grind against AMAT.

Deleted member 431298

May I suggest that we have a look at the topic at hand from a slightly different approach: What do the experts say about the side effect profile of AMAT, and what are the popular descriptions of the side effects profile of the AMAT drugs?
One statement from William Chamberlain, commenting the Selby et. al. study:

[...] The data support another interpretation: AMAT provides a more effective treatment regimen with a more favorable side effect profile than current conventional therapy. [...]

Granted, Chamberlain treats patients with AMAT himself, so he may be biased, but it does seem like the Selby study at least did not report any severe side effects.

AMAT drug side effects, as written on www.medicinenet.com:
(Note: any cocktail effect is not taken into consideration)

Side effects for clofazimine
More common side effects include: loss of appetite, diarrhea, nausea, vomiting, dry skin and discoloration (from pink to brownish-black) of the skin, stools, urine, saliva, sweat, tears or lining of the eyelids. Other side effects reported are changes in taste, dry or irritated eyes, headache, fever, increased blood sugar and an increased sensitivity to sunlight.

Clarithromycin is generally is well tolerated, and side effects usually are mild and transient. Common side effects of clarithromycin are: nausea, diarrhea, abnormal taste, dyspepsia, abdominal pain and headache.
Other important side effects which are rare, but serious include:
liver failure, hearing loss, and seizures.
Clarithromycin should be avoided by patients known to be allergic to clarithromycin or other chemically-related macrolide antibiotics, such as erythromycin. Treatment with clarithromycin and other antibiotics can alter the normal bacteria flora of the colon and permit overgrowth of C. difficile, a bacterium responsible for pseudomembranous colitis. Patients who develop pseudomembranous colitis as a result of antibiotics treatment may experience diarrhea, abdominal pain, fever, and sometimes even shock.

side effects: Diarrhea, stomach upset, changes in taste, or nausea/vomiting may occur. If any of these effects persist or worsen, tell your doctor or pharmacist promptly.This medication may cause urine, sweat, saliva, or tears to turn brown-orange. This effect is harmless and will disappear when the medication is stopped. However, dentures and contact lenses may be permanently stained. Remember that your doctor has prescribed this medication because he or she has judged that the benefit to you is greater than the risk of side effects. Many people using this medication do not have serious side effects. Tell your doctor immediately if any of these rare but serious side effects occur: easy bleeding/bruising, signs of a new infection (such as fever, persistent sore throat/cough), muscle weakness/pain, joint pain/swelling, eye pain/redness, vision problems, chest pain/pressure, persistent nausea/vomiting, unusual weakness/tiredness, dark urine, yellowing eyes/skin.This medication may rarely cause a severe intestinal condition (Clostridium difficile-associated diarrhea) due to a type of resistant bacteria. This condition may occur during treatment or weeks to months after treatment has stopped. Do not use anti-diarrhea products or narcotic pain medications if you have any of the following symptoms because these products may make them worse. Tell your doctor immediately if you develop: persistent diarrhea, abdominal or stomach pain/cramping, blood/mucus in your stool.A very serious allergic reaction to this drug is rare. However, seek immediate medical attention if you notice any symptoms of a serious allergic reaction, including: rash, itching/swelling (especially of the face/tongue/throat), severe dizziness, trouble breathing.This is not a complete list of possible side effects.
Love it Ole. Very informative. Knowing how they react together though is important. I know from the research done by Naser and crew in vitro that the triple combo in RHB104 has some synergistic type effect. Studies posted below. I've also been told to space the rifampin as far from the clarithromycin as possible since it can speed up the clarithro metabolism and lower the clinical level in the bloodstream. I believe the RedHill pill uses a buffering system with PEG or possibly a capsule inside a capsule (the patent was very hard to understand!) to combat this effect.

The AMAT docs have told me that the side effects of AMAT, while possible, are not as serious or common as those of biologics. I know they're probably biased, but they've also treated a lot of patients. Long term is an issue that concerns me, but I know some TB patients take them for years, so at least there is that data available, as well as the few reported of CD patients. As has been mentioned, it's a risk/benefit analysis to discuss with your docs.

These articles suggest that bactericidal antibiotics[1] may increase oxidative stress. In addition to supplementing with probiotics, it might be a good idea to take antioxidants and eat an especially anti-oxidant rich diet if you are using the long term antibiotic therapy. This might help fighting with the ROS build up.

[1]: General info on this: https://courses.lumenlearning.com/boundless-microbiology/chapter/overview-of-antimicrobial-therapy/

Antimycobacterial agents were evaluated with respect to their bacteriostatic activity (growth inhibition) versus the bactericidal activity: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1140486/

Deleted member 431298

Short update to my MAP-levels-trend-experiment:
The MAP culturing process has now started. At the same time the blood was drawn, a week ago, I had a Calprotectin test done. Results just came back elevated: 285 ug/g. That is consistent with my symptoms. Tests earlier this year while on Methotrexate have been <100 ug/g, indicating remission.
After the tests I started Methotrexate 12.5mg/week orally. Diarrhea has already gone, and I feel better.
It will be very interesting for me to learn if the flare has led to an increased number of M. Paratuberculosis bacteria in my blood. I will post the results when they arrive.

In the meantime I found a very interesting study testing the action of Methotrexate and 6-MP on MAP in vitro (in the lab). The study found Methotrexate to inhibit MAP growth almost as effectively as Clarithomycin, 6-MP somewhat less.
Maybe Methotrexate should also be called Anti-MAP therapy? :)


The study propose that the primary action of Methotrexate and 6-MP in IBD to kill MAP bacteria:

Both methotrexate and 6-MP interfere with DNA replication. Methotrexate acts by inhibiting dihydrofolate reductase, folate generation and the consequent production of adenine.[12] The mechanism of action of 6-MP is to substitute for guanine in DNA replication.[12] Because prokaryotes (simple cells, such as bacteria, OleJ's comment) must synthesize their own folic acid, they should be more susceptible to folate inhibition than eukaryotes. (More complex cells, such as human cells, OleJ's comment)

Deleted member 431298

Adverse events during two years of AMAT treatment of around 100 patients in the 2007 Selby study

Adverse Events
Overall, the treatment was well tolerated; only 16
subjects were withdrawn because of an adverse event: 8 in
each group, including 5 each in the induction phase.
Several adverse events were significantly more common
in the antibiotic group than the placebo group during
the induction phase: abnormal liver function (2.3% vs
0.3%, respectively), vaginal candidiasis (4.0% vs 0.8%, respectively),
abdominal distention (3.4% vs 0.8%, respectively),
myalgia (2.3% vs 0.3%, respectively), and urine
discoloration (2.8% vs 0.3%, respectively). Between weeks
17 and 52, arthralgia (3.5% vs 1.2%, respectively) and
tooth discolouration (2.3% vs 0.2%, respectively) were the
only adverse events significantly more common in those
on antibiotics than on placebo. The number needed to
harm during the induction phase was 77 and, for the
whole study, 40.

Deleted member 431298

Guerrero, I know there are reports of allergic reactions and serious infections but don't have the statistics. Also, I suspect not all adverse effects are registered, because there is no way of proving that Remicade caused them. I got a very serious infection in my kidneys, and it is unclear if that came from Anti-TNFa or Crohns. It has to be said I had been on Remicade and later Humira constantly since year 2000.

Deleted member 431298

Another note: Could the Redhill Anti-MAP therapy study be flawed??
Learning that Methotrexate (MTX) and 6-MP have Anti-Map effects in vitro made me think if they are allowed as a supplemental treatment in the Redhill Study. And--- YES THEY ARE!

The same researcher (Greenstein) who reported the Anti-MAP effect of MTX and 6-MP(I linked to the study above) has actually warned about this in this commentary.
This is bad news. It could mean the therapeutic effect of the Anti-MAP antibiotics do not stand out over the other drugs given to both arms in the study.
Ole - that has been a common issue and came up at the Philly conference. There was some debate on Dr. Greenstein's methods as well, which hasn't been reproduced. Ultimately, I don't think you see a lot of patients jumping up and down saying their CD was healed by 6MP or MTX, though they both do seem to help some. If you add on Rhb-104 to those, and people do incredibly well, then you'd have to conclude it was the RHB that was doing the bulk of the healing. Keep in mind, a lot of the patients in the RedHill trial had already been on a therapy for a while and still had moderate to severe CD to qualify for the study. So it's not like their current therapy is doing all that much.

I am a long term Crohn’s sufferer and I am looking for information about Dr Jeremy Sanderson ant the anti-MAP therapy. After trying and failing immunosuppression I read about this new therapy in the Human Para Foundation website where Dr Sanderson’s was mentioned. I understand he is one of the few doctors in the world who provide anti-MAP therapy. I would be grateful if anybody who is being treated or has been treated by him could share their experience so I can get some feedback before I decide whether to make an appointment. I am especially interested in hearing from people who see him in private and/or from outside the UK. I am not a UK resident so things would be more complicated for me.

Thank you

(I hope I posted in the right thread)
Are you in Europe Crohnsufferer? Have you looked for docs in your local area? I know Dr. Sanderson sees private patients at the Shard building location and I've heard good things.

These articles suggest that bactericidal antibiotics[1] may increase oxidative stress. In addition to supplementing with probiotics, it might be a good idea to take antioxidants and eat an especially anti-oxidant rich diet if you are using the long term antibiotic therapy. This might help fighting with the ROS build up.

[1]: General info on this: https://courses.lumenlearning.com/boundless-microbiology/chapter/overview-of-antimicrobial-therapy/

Antimycobacterial agents were evaluated with respect to their bacteriostatic activity (growth inhibition) versus the bactericidal activity: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1140486/
"How do antibiotics affect human mitochondrial function, especially on the long term?" I've been wondering about this for some time.

First, read this: Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. The Origin and Evolution of Cells.

Endosymbiosis: https://en.wikipedia.org/wiki/Symbiogenesis

Indeed, mitochondria, the organelles responsible for energy production in the cell, have bacteria-like DNA and other molecules, suggesting that mitochondria are the product of an ancient endosymbiotic event, in which a bacterium was engulfed by another cell. The important implication of this, said Ronald DePinho, president of the MD Anderson Cancer Centre in Houston, Texas, who also did not participate in the research, is that “drugs targeted to [bacterial] physiology might also impinge on mitochondrial biology.”
and a comment on this report:
In additon to the disruption of normal ROS signalling pathways mentioned in this paper many antibiotics have two other deleterious effects in human cells. They decrease respiratory competence and shift cell populations to aerobic glycolysis (the Warburg effect) resulting in localized lactic acidosis and a microenviroment favorable to tumor formation, tissue invasion and metastasis. In addition increased poduction of ROS is mutagenic to both nDNA and mtDNA destabilizing both genomes, decreasing mitochondrial survellance and clearing of tumorigenic karyotypes in the nucleus by the intrinsic apoptotic pathway, both hallmark features of cancer. I suggest (in agreement with many other investigators) that such antibiotics are carcinogenic and thus the findings reported here are very clinically relevant especially when administered for chronic infection. We need to find alternative antimicrobial therapies for non life threatening infections that do not harm these patients.

https://medicalxpress.com/news/2015-03-antibiotics-unexpected-effects-mitochondria.html (the same story)


These are discussed in the context of healthy populations; but when you think about the findings on Crohn's and mitochondrial dysfunction, this becomes even more important.

Mitochondrial dysfunction in inflammatory bowel disease

Mitochondrial dysfunction, persistent oxidative damage, and catalase inhibition in immune cells of naïve and treated Crohn's disease.

Next two articles (below) sort of explain why anti-tnf's work in Crohn's, and why they do better than the traditional immunosuppressants on tissue healing:

Role of oxidative stress and antioxidant enzymes in Crohn’s disease

Mitochondrial Dysfunction in a Patient with Crohn Disease: Possible Role in Pathogenesis

"Gene that affects cell power supply may hold key to bowel disease"

"Studying the role of damaged mitochondria in causing Inflammatory Bowel Disease."
Hi irishgal,
yes I am in Europe and unfortunately there are no doctors in my area who prescribe anti-MAP therapy. It won't be too difficult for me to go to London but it is expensive so I wanted to make sure I found the right doctor and that he is good at what he does.
I suggest everyone ignore Crohn2357. He's just here to troll with scary research and not really have a genuine discussion about the clinical experiences with AMAT. I wish the mods would do something about it. What matters more is what IBD patients on AMAT are saying. Random research about the dangers of antibiotics is not very helpful. We need to look at the clinical data.

As for me, an update... I started AMAT 4 days ago. The herx reaction is very intense. Mind you, I have ulcerative colitis and not CD so my experience may be different. I started at full dose - 500mg clarithromycin 2x daily, clofazimine 100mg 1x daily, rifampin 300mg 2x daily.

The reason why I chose to start at full dose is because the most experienced doctors with AMAT recommend it in order to avoid bacterial resistance.

I'm also taking LDN 3mg.

So far the harshest effects are on my bowels. I was already at the tail end of a flare but now my bleeding and pain have increased. However, I'm not flaring. I think the drugs are just really irritating to the GI. The other effect I'm noticing is that my face is extremely dry and inflamed, which I have heard is a side effect of clofaz, but it may also be a herx reaction. Either way it's too soon to tell. I've been moisturizing 3-4 times a day and it doesn't seem to be helping. I am also a lot more dry in general.

I am getting blood work done this afternoon to see where my body is at. My biggest concern right now is that my hemoglobin was already on the lower side before this, and if it's getting too low from the increased bleeding I may have to consider stopping. However, if the bleeding is a result of a herx, it should get better after these first two weeks. The general suggestion I've been given is that if I can tolerate the meds for 1 month, but if after that 1 month I'm not improving, then I should probably stop.

I've upped my probiotics a lot. There are mixed opinions on this. Some say to wait for the initial die off to stop before adding pros, others say you need to be doing pros between antibiotic doses to avoid c. diff. The clinical literature on AMAT and c. diff seems to indicate that it's actually rather rare, unless you were already prone to it.

Two days ago I received a glutathione IV from a naturopath, and I have started taking milk thistle twice daily. I'm trying to give my body as much liver protection and detoxing capacity as I can.

I considered starting with levofloxacin instead of clofazimine but the black box warning about tendon ruptures from the fluoroquinolone family of drugs made me opt against it. It does tendon damage to 100% of people who take it, it's just that in some the damage manifests as actual symptoms. I've read many horror stories. I would not take a fluoroquinolone unless it's literally a life and death situation. Clofazimine on the other hand is also a very harsh drug. The clinical data shows 50% of people who take it end up stopping it. My intuitive sense is that, of the three I'm taking, clofaz is causing the most problems.

On the whole though, my symptoms are not as bad as they could be. No nausea, thank god. For me nausea is a deal breaker. So far it's lower GI symptoms + face dryness, and if these get better as time goes on then I think I can live with this protocol.

Down the road I'm also looking into fecal transplant. UC'ers tend to do well with those, and I'll need to replenish my bowel flora after all these antibiotics.
My mycobacterial infection was diagnosed by Otakaro Lab in New Zealand. Right now it's the most accurate method available. The Crohn's Vaccine development program is also creating an accompanying rapid MAP test that will be available in the future, but for now Otakaro is the best we've got. There are other labs in the world that test for MAP using blood PCR assays, but they aren't as accurate. You really need to culture blood to find the MAP, and MAP has very specific requirements to be seen in a culture.

It's difficult in general to run a PCR assay on MAP because researchers are still figuring out the best RNA sequences for identifying it. Otarko has identified active mycobacteria in my blood, but whether or not they are MAP is not certain. However, because the infection is active and my IBD is refractory, I decided to give AMAT a try anyway. The difficulty with UC and MAP is that UC patients tend to have the same numbers of mycobacteria as the healthy control group, so MAP may not be the causative factor of UC, but rather a complicating factor. Most healthy people have some mycobacteria in their bodies. They are ubiquitous in the environment. However, people with IBD have some kind of immune deficiency which can't prevent the mycos from causing harm, especially in CD patients. However, some UC patients go into remission with AMAT. I think if you're a CD patient you have a much higher chance of this successfully working.

I'll post more updates later in my treatment.
Good luck with your treatment Connor. Let us now how you do. I know the beginning is pretty rough, especially if you start full strength. I did as well, mostly because that's what my doc told me, and I didn't know any better. But with my case, it got all of the horrible effects out of the way in the beginning during the die off and I think it killed any MAP that was active at the time, which I think was a bunch per my culture (also from Otakaro.) Crossing my fingers it works spectacularly for you!

Deleted member 431298

Good luck Conner, and thank you for updating us here.
Crohnssufferer: I also considered contacting Dr. Jeremy Sanderson, I even got my GI to write up a referral document (which is required to get an appointment) but I am also afraid of the cost, and I want to get the results of a blood culture test first. I will update you if I go ahead.
Irishgal - Good to hear is topic was covered in Philly. In an optimal study design though it seems a solid MAP culture test of subjects prior to AMAT, and more research on the effect of MTX and 6MP would have been nice gauges for the efficacy.
Just a little update. I'm one week in and having a hard time. My bowels are extremely irritated by the antibiotics. I had to cut out clofazimine for a little while and just stick to clarithro and rifa. Even so, I am bleeding a lot and my CRP went from less than 1 to 35. I'm getting an iron IV today.

As a result I've had to start prednisone again. I'm doing a low dose of 10mg, and I'm taking DHEA with it. Last year I had to do a different triple therapy to get rid of b. hominis and aeromonas, and within two days of taking abx for it my bowels became so healthy. But this time... I'm not so sure.

I'm giving it the standard 2 weeks to see if it's just die off or I really can't tolerate this therapy. So far I am leaning to the latter. My symptoms are a throw-back to 2 months ago, although I don't seem to be flaring for real. It just seems like major irritation of the mucosa that has barely had a chance to heal.

I'd recommend that anyone starting this therapy who knows they are sensitive to abx should do the ramping up method rather than starting at full dose. Other than my bowels, I have no other intolerance symptoms. No nausea, nothing.

Deleted member 431298

Conner, thank you so much for your honest update. Information like this is really valuable to me, and I presume, to others following this thread. I am sorry to hear you are having such a hard time. I cross my fingers it is the herx reaction and/or your system adjusting to the antibiotics, and the symptoms will fade. Keep us posted if able, and good luck.

Deleted member 431298

Irishgal, I wonder if you know why the Greenstein study on 6MP/MTX as MAP inhibitors was not reproduced?
Was it because no one ever tried?
Or was it that others tried but were unable to get the same results?

I came across this intersting study about anaerobic adaptation of MAP (from 2017)

The conclusion says:

[...] a number of investigators have demonstrated dose-dependent inhibition of MAP in culture by a number of anti-inflammatory drugs including methotrexate and 6-mercaptopurine [37, 38, 39, 40, 41, 42, 43, 44]. As a result, Greenstein et al. postulated that treatment of patients with inflammatory bowel disease with methotrexate and 6-mercaptopurine may result in inhibition of MAP and secondarily a decrease in pro-inflammatory cytokines [42]. In the current study, testing of anti-inflammatory drugs was beyond the scope of this project. However, future studies are planned which will determine the activity of anti-inflammatory drugs against MAP under both aerobic and anaerobic conditions

I will read up on the refs. 37-44 to see what they say about this matter.

Apart from this observation re. MAP and 6MP/MTS, the article is a very interesting read. The researchers suggest the reason AMAT is unable to clear the MAP infection completely may be that the MAP bacteria can take on an anaerobic state, where the drugs cannot reach the bacteria.
Last edited by a moderator:
Ole - this is a bit of heresay, but I believe it was tried and was not able to be reproduced. Something about the lab equipment used??
And if you want to watch Dr. Parrish's presentation on her work you mentioned above, about anaerobic adaptation of MAP, it's on the site. She was supposed to present in Philly, but had to cancel at the last minute. However, she kindly recorded her talk with a colleague and provided it to us to post! And they are out of Johns Hopkins.

MAP is a pretty great mutator. Very hard to kill. This is the type of stuff you see with TB.

Deleted member 431298

I watched to video with Dr. Perrish, thank you for pointing to that. Very exiting stuff, and I am encouraged to learn experienced microbiologists and TB specialists like her (and Marcel Behr) are doing research on the MAP-CD connection.

Irishgal: Out of curiosity - did your doctor (or yourself) ever consider adding an anaerobically effective antibiotics (metronidazole) to the regimen? I am in no way competent to suggest whether it would be a good idea...

A few thoughts on Methotrexate and the Jarisch-Herxheimer reaction
Then on to an anecdote about myself, which leads me to speculate whether MTX can result in a (small) Jerisch-Herxheimer reaction. So I took a break from MTX monotherapy over the last two month, to see if if my MAP levels would increase. I got CD symptoms, elevated calprotectin, shipped of blood for MAP culturing, and two weeks ago I started MTX again.

Yesterday morning I took my second dose of 12,5mg once a week. I felt weak towards evening time, went to bed early, and woke up at 2:30AM feeling like crap. Low grade fever, nausea, and stomach discomfort. Between 2:30 and 4:30AM I went to the toilet like six times and almost vomited.
That is so strange, I thought. Usually that dose would result in a lack of appetite for half a day or so, maybe some nausea, but definitely nothing like this, and never a sudden onset of diarrhea and urgency.
Interestingly I had a similar reaction, and an really awful night a week ago- the night following the first dose of MTX after restarting.
Last week I did not think much of it, and apart from a truly shitty appx. 24 hours, the following days I felt fine with normal BM's.

But last night, when the symptoms reoccurred, I started speculating about why I got so fierce symptoms from MTX, and I thought of Conner's description of what is possibly a Jerisch- Herxheimer reaction in this thread.

So last night I looked into the Herx reaction, and found the article: Jarisch–Herxheimer reaction: paradoxical worsening of tuberculosis chorioretinitis following initiation of antituberculous therapy

In the article they describe that Prednisolone dampens the symptoms, so at around 4:30 I took 12,5 mg prednisolone.
About an hour later I felt the stomach settle down, and I was able to go to sleep. This morning I feel fine, hungry, and my stomach is calm. It seems I have had quicker resolution of symptoms than last week, where I felt bad the following day too.

Although this is just an anecdote, I can't help but wonder if I am experiencing the Herx reaction because MTX is targeting more live MAP bacteria now that I have been off it for two month.
Last edited by a moderator:
Ole - I have actually had great success with flagyl over my 25 years of dealing with CD. It was the only thing that worked really well and I was on and off of it many times. I'd get much better, but then would have to come off and the CD would return. When I started AMAT, I figured it was better than flagyl since none of this research was available at the time. Now, Dr. Borody uses flagyl as a 4th sometime, or it's cousin tinidazole which I think is a safer alternative. Since flagyl causes nerve damage and other side effects, it's not safe for long term use, so if I relapse, a course of that will certainly be in the cards - maybe with clofaz. But I was doing so well at the time, I never thought about adding another antibiotic since I didn't want to mess with success. Still doing well, so no need to add more meds if the current ones are keeping the MAP under control.
If rifaximin worked for me does that mean the anti map antis will also work?
Not necessarily. Rifaximin I think is for people with SIBO and IBS. It's in the same family as rifabutin and rifampin, so it could be a clue that you may have a MAP infection, but the best way to know for sure is to send a sample to Otakaro Pathways and get tested. If you come up with MAP, maybe your doc would consider AMAT on the premise that rifaximin worked well. If you've run out of all other therapies, it's an easier sell too.
How do people who are using (or considering to use) the anti-map therapy find clofazimine?

This is an important issue.
How do people who are using (or considering to use) the anti-map therapy find clofazimine?

This is an important issue.
If you are in the US, you can get a script from your doctor and fill it at an online pharmacy in Canada using Pharmacy Checker. That's the easiest way, though I know a couple of people who get it from India and Switzerland. Not sure about other countries. I know it's very difficult to get if you live in Canada.

Deleted member 431298

To Conner:
How are you doing? Good I hope!. If you would consider giving us a heads up I'd be greatful. Cheers
If you are in the US, you can get a script from your doctor and fill it at an online pharmacy in Canada using Pharmacy Checker. That's the easiest way, though I know a couple of people who get it from India and Switzerland. Not sure about other countries. I know it's very difficult to get if you live in Canada.
This video shows the adress of a pharmacy in Switzerland which is said to have clofazimine. It can be seen at 14.25.
To Conner:
How are you doing? Good I hope!. If you would consider giving us a heads up I'd be greatful. Cheers
I'm 1 month in and all bleeding has stopped. Stools became formed so quickly that they are actually causing bleeding, but the bleeding is not related to UC. CRP is in normal range now. I can finally start to get off prednisone.

Because I stopped taking clofazimine, I am looking into a 3rd drug to replace it. I may use tinidazole, but I'm not sure yet. Even at low doses, I don't see how I could tolerate an azole drug for months. They're really hard on the body.

There was a time a couple weeks back when I felt like my body was on toxic overload and I didn't know how to deal with it. My liver and kidneys felt sluggish. Then one day I was at the grocery store and I saw beet sauerkraut, unpasteurized, and I found myself craving it. I went home and literally ate half the jar, which is insanely fibrous for someone with UC.

Within a couple days my body aches and pains, skin issues, sluggishness and fatigue all died down. So now I have a bit every day. I think it's the glutathione in beets that must be helping. Glutathione scavenges the body for reactive oxygen species, which is what AMAT releases to kill organisms.

Over all I am happy that I started AMAT and I seem to be tolerating it much better now. But man, the first couple of weeks were hell!

Deleted member 431298

Conner, I'm so glad to hear you are past the first rough week. Wish you smooth sailin' from now on :)

To recap my story: was in remission this spring, on medication (calprotectin <100, no symptoms). Got a MAP culture test done that came back positive, but with very low numbers of live bacteria. Got off dairy and cow's meat and tried to taper and stop medication. Got sick in september (calprotectin close to 300, diarrhea).

Latest news:
Sent of another blood sample for culturing a month ago while I was sick, before restarting medication - and it just came back positive, with significantly higher numbers of live bacterias present than the first test.
Food for thought...
Last edited by a moderator:
The numbers are always higher during a flare because that's when they're active and reproducing. They create biofilms and peptidoglycans which induce inflammatory responses in the body.

During periods when you're healthy and strong they will be dormant and in smaller numbers.

Deleted member 431298

here's the results of the two tests compared. It would be very interesting to hear what other's results are / was (staining bacteria, pct. at 7 and 30 days).

[EDIT: WOW this was my post number 100 :) ]

Last edited by a moderator:
That's a handy bar graph. I don't have something so visually laid out, though I guess when I get my second round of blood work cultured I will be able to draw comparisons.

You have way more large forms than I did in my test, but I have UC and you have CD. The highest I had was 6%. If MAP is the reason for my UC, then it's crazy that my body is reacting to such small numbers. However, it would, given how sensitive my immune system has always been.

Can I ask where you got your culture done, Ole J?

Deleted member 431298

The test was done by Otakato Pathways in New Zealand. Where did you get yours done? If you do a second test I'd be really interested in knowing your MAP levels trend. Maybe initial value can be different based on your UC diagnosis and immune system, but I am guessing there should be a decline in numbers if MAP is a causative agent.

In the conclusion of the test from may, they wrote:
The overall appearance is similar to that seen in Crohn's disease, where the patient is in remission or on prolonged therapy.

In the conclusion of the test from october, they wrote:
The overall appearance is similar to that seen in Crohn's disease where the patient may be on a sub-optimal therapy. There is some indication of growth suppression and no appreciable increase in ruptured forms.

The graphs are easy do draw in Excel if you know that program. I did it manually, filling cells with color to represent the bars.
Last edited by a moderator:
For patients who want to try (or learn more about) Anti-MAP therapy, Dr. Chamberlin says they "are building a private database of practitioners and will assist if possible".

Full quote:
Help! My doctor won't prescribe AMAT. What do I do?
This is currently one of the most common practical questions I get. First try providing your GI or general practice doctor with the Core Research Pack on this site, and then requesting that they consider prescribing AMAT once they are fully informed. Better still, have them view the videos on the website. Of course, I would be happy to evaluate you in my office in New Mexico if you are able to travel to see me. If that is impossible, check the RedHill trial sites for a location near you. There are supervising doctors at each site, many of whom have their own GI practices. They would be familiar with AMAT and would be able to discuss it with you. Alternatively, integrative or functional health doctors are generally open minded practitioners and many patients have had success once they are provided the research. If you have exhausted all of these options, please contact TheCrohnsInfection.org as we are building a private database of practitioners and will assist if possible.
Taken from: https://humanpara.org/anti-map-qa/

The link he gave has changed. To contact them, you should go to this link: http://humanpara.org/contact/
Crohn2357- In regard to the above info about finding an AMAT doc, that is one of the biggest challenges people who want AMAT face now. Understandably, since it's not fully approved and considered off label, and we live in a fairly litigious society. Hopefully this is just a stop gap measure until RedHill is approved.

And just as a little background, the website changed from The Crohns Infection to Human Para when it became an IRS nonprofit. Prior to that it was just some of us trying to put out good info to people who needed it, but we couldn't do much since we didn't have funding. Now, as a nonprofit we can do things like sponsor conferences and research, and give people tax credit for donations. We have the ability to actually move this forward as a legitimate organization. Also, we decided we wanted to focus more on MAP diseases and not just Crohn's, so that was another reason for the naming switch. 😀

We do in fact keep a private list of doctors around the world that patients contribute to since we get a LOT of inquiries from patients asking for a doctor in their area. The privacy is required because we certainly don't want anyone to get in trouble for prescribing off label. Also, prescribing AMAT is very situational, so a doc may not want to be known for prescribing AMAT and have patients demand that if it's not right for their case. The best we can offer is that these docs may have some familiarity with MAP science and may be open to reading the research. Integrative health docs also seem to be more open minded as well.
irishgal - I agree with the necessity of the precautions you have taken.

For patients (or loved ones) who are reading this support group: If you have tried all the conventional medications without achieving remission, you have a greater chance of using off label treatments. At that point, I think it would be wise to send your blood samples to Otakaro Pathways and get tested for MAP. If the test result comes back positive, at least you and your doctor will have another justification (the other being having a treatment-reftactory disease) for using an off-label treatment (like anti-MAP therapy).

According to Dr. Chamberlin, "there is a 20 year body of peer reviewed research which indicates that AMAT is as effective as other Crohn’s therapies in inducing remission"[1]. In addition to your blood culture report, show your doctor the compiled literature and resources on the MAP hypothesis[2] .

That's my two cents.

[1]: Source: https://humanpara.org/anti-map-qa/

[2]: You can find these on the first post of this support group.
Last edited:

Deleted member 431298

You have way more large forms than I did in my test,
Conner - after your comment I rechecked my graph and realised I made a mistake in representing the numbers. The graphs show the AVERAGE percentage of growth in each petri dish (four and five dishes cultured respectively in May and in October.
When I wrote the percentage as numbers below the graph, I forgot to divide the sum with the number of dishes. That means, the average number of different forms is way lower than the numbers written (eg. average large forms after 30 days, October = six percent, not 30). I corrected the graph. (This mistake does not change the trend)
Last edited by a moderator:
irishgal - There is no "send" button for sending a message to Human Paratuberculosis Foundation on the contact page.

Edit: I see the "submit" button near the spam check feature (calculation question) now; but it is not visible if you don't put your mouse on it.
Last edited:
irishgal - There is no "send" button for sending a message to Human Paratuberculosis Foundation on the contact page.

Edit: I see the "submit" button near the spam check feature (calculation question) now; but it is not visible if you don't put your mouse on it.
Weird - I bet this is due to the latest WP update they just did that was huge. I see whta you mean. Looks ilke they switched the color on us for that form. I'll check into it and hopefully get it back to normal!
I will probably start the Anti-MAP therapy in a month's time.


1)According to this page:
From patients who have provided this information publicly, the most commonly used daily AMAT protocol is: 1000 mg. of clarithromycin, 300 mg. of Rifabutin, 2 mg. per kg. of clofazimine. These doses are split in half and taken throughout the day. Some doctors prefer to ramp up this therapy to minimize initial side effects, starting with lower doses and gradually increasing the strength to the full dose over time.
Does Dr. Borody use this protocol?
2)I've read that Dr. Chamberlin uses different antibiotics, does anyone know why? Anyone know his protocol exactly?
3)Dr. Chamberlin states:
I've heard some doctors start all of the medication at full strength on the first day, and some start with lower doses and gradually increase over time to the full dose. What are the benefits and drawbacks to each method?
I start my patients on the full dose on Day 1 to minimize the risk of bacterial resistance. This produces more common side effects, including nausea and feeling like you have the flu for a few weeks, but I believe this approach works well for the majority of patients. The doctors who choose to slowly increase the dosage over a period of weeks do so to minimize side effects for the patient. There may be some cases of patients who have recurrent obstructions or more severe side effects initially where I would consider a ramp up method, but no studies have been done to compare these methods side by side. Therefore, which method is superior is up to each practitioner’s opinion.
Which one is better, do you think? What do others (patients and physicians) think about this? Which method is more commonly used? Which method does Dr. Borody use these days?
4) Can I use 6-mp and the triple antibiotics (Clarithromycin, rifabutin, clofazimine) together? Do you know any patients who are using these together?
5)Which side effects are common?
6)Does the altered taste perception and metallic taste in mouth (associated with clarithromycin) get better in time?
7)I am prone to migraines and headaches in general, do you know if any of these antibiotics causes headaches (I know some antibiotics do), based on your or others' experiences?
8)I have read some patients use flagyl as the 4th antibiotic; how common and necessary is this? Do you know any other antibiotics that can be used as the 4th agent (ethambutol?, for example)?
9)Do you think prebiotic and probiotic supplementation is necessary? Do you have any specific recommendations with these?
10)Which antibiotics should be taken on empty stomach, which ones should be taken with food?
11)What is the generally accepted time-period to assess the efficacy of the treatment?
Conner - after your comment I rechecked my graph and realised I made a mistake in representing the numbers. The graphs show the AVERAGE percentage of growth in each petri dish (four and five dishes cultured respectively in May and in October.
When I wrote the percentage as numbers below the graph, I forgot to divide the sum with the number of dishes. That means, the average number of different forms is way lower than the numbers written (eg. average large forms after 30 days, October = six percent, not 30). I corrected the graph. (This mistake does not change the trend)
I also got my blood done Otakaro. The conclusion that was drawn was that I was in active flare status or sub-optimal control. The presentation was identical to that of Crohn's patients, except I have received a dx of UC.

Your numbers also match mine then, and you have CD. So this is all very fascinating.

According to one theory I've read, adults who are infected with MAP tend to develop UC, not CD. Children exposed to MAP tend to develop CD.

My UC is severe. Every flare becomes fulminant, even with prednisone and hospitalization. I've refused surgery every time because I've known in my heart that an infection is somehow involved and I was only able to prove it with Otakaro two months ago!
Crohn2357 - these are all great questions to ask on the Human Para Facebook private group or to discuss with your prescribing doc. AMAT is very situational, and a lot of the general info is given on Human Para, but each doc really needs to decide what's best for their own patient. I know Dr. Chamberlin will consult with other docs when requested, and I think Dr. Borody does too. The patient stories on Human Para may also give you some idea of what to expect in the way of side effects. Good luck!

Deleted member 431298

I will probably start the Anti-MAP therapy in a month's time.


Very relevan questions! I hope that over time, as more of us manage to try AMAT, we will be able to have some of the answers in here.
Also thanks for sharing you plans. I am curious to hear if (and how) you managed to get your GP / GI on board?
I tried to get my GI to read up on the core research pack at human para, but he never did and now he has quit. I am waiting for another one to start in January, and then I will ask if I too can try AMAT.
Also thanks for sharing you plans. I am curious to hear if (and how) you managed to get your GP / GI on board?
I have inflammation and narrowing in my rectum and I am considered non-responsive to conventional treatments. I am facing another resection surgery, which would leave me with a permanent stoma.

At this point, I did what I suggested in this post.

You can send a private message to irishgal or humanpara.org asking for a doctor who is open-minded about this treatment and is near you.

irishgal - In regards to the dosing of Rifabutin, I have found conflicting statements on Dr. Borody's treatment protocol from different sources. Here are some examples:

PARA: Can you describe your treatment protocol?
Dr. Borody:
Our treatment consists of a combination of Clarithromycin, Rifabutin and Clofazimine. We commence treatment at a lower dose and raise to a higher dose after four weeks to try to avoid any profound side effects that can occur if we go to a high dose immediately. Following baseline studies of patients including blood workup, cross sectional ultrasound of small bowel (if small bowel is involved), inflammatory leucocyte bowel scan, colonoscopy with biopsies and photography, and small bowel X-ray if relevant - we then go on to commence the patient on the anti-MAP antibiotics. They are started with a dose of Rifabutin 150mg twice daily with food, combined with Clarithromycin 250mg twice daily and Clofazimine 50mg twice daily. Second weekly the patients undergo full blood count and liver function tests to monitor changes, especially in white cell count, neutrophil levels and liver function test elevations.

Generally speaking most patients have a minimal drop in white cell count, but many of these patients, being so ill, have highly elevated white cell count, so that this never reaches a leucopenia level. In three of twelve patients, when initially treated, we did reach leucopenia which was just below the level of normality, but we did not have to stop the medication in any of these because of our stepwise elevation of drugs. If this did occur, we planned to reduce the Rifabutin and Clarithromycin dosage down to 50% until the white cells recover. At four weeks the dose then goes up to 300mg of Rifabutin in the morning and 150mg at night and 250mg of Clarithromycin in the morning and 500mg at night. We use a high dose of Clarithromycin at night, to reduce the metallic taste which Clarithromycin can cause. For the next 24 months the patients are maintained on this treatment, progressively reducing and ceasing steroids and other Crohn's treatments.

Borody's current protocol dosing is 1000mg clarithromycin, 600mg rifabutin (slowly ramped up from an initial 300mg over 3-4 months), and 150mg clofazimine (2mg/kg as Doug said).

3) This is from Humanpara.org. I understand that this does not specifically point out to Dr. Borody's protocol, but nevertheless, this suggests another different protocol.

From patients who have provided this information publicly, the most commonly used daily AMAT protocol is: 1000 mg. of clarithromycin, 300 mg. of Rifabutin, 2 mg. per kg. of clofazimine. These doses are split in half and taken throughout the day. Some doctors prefer to ramp up this therapy to minimize initial side effects, starting with lower doses and gradually increasing the strength to the full dose over time.

4) Again, from the same source above. This is the RHB-104 dosage, which was suggested by Dr. Borody If I am not mistaken.
RedHill gradually increases the dosage, with each capsule containing 95 mg clarithromycin, 45 mg Rifabutin, and 10 mg clofazimine. Eventually, the patient will take 5 capsules, twice a day for a total dosage of 950 mg. of clarithromycin, 450 mg. of Rifabutin, and 100 mg. of clofazimine.
Do you know what is his current protocol now? Dr. Borody is off on sick leave until the 1st of March, so I can't reach him.

I would appreciate your (and others', if anyone knows) input on this.
Last edited:
Regarding rifabutin, there may have been some confusion early on about rifabutin vs. rifampin dosage. I clarified with Dr. Chamberlin recently, and he said it was generally 300 mg daily rifabutin, 600 mg daily of rifampin. Patients take one or the other. However, he also mentioned RedHill would sometimes use 450mg rifabutin, and they have done a lot of research on dosages. So definitely not 600mg rifabutin!

Deleted member 431298

Some thoughts on short-chain fatty acids (SCFA, such as acetate, propionate, and butyrate) and MAP.

I realise this might seem a bit off the main topic of this thread, but on the other hand: What if SCFA's in some way inhibit MAP growth?

Science is currently focusing on the production of SCFA in the colon as a mechnism that may reduce inflammation. Interestingly
one study by R Arrazuria et. al found the butyrate-producing bacteria species Anaerostipes to be negatively associated with MAP infection.

Not a whole lot of data I admit, but in order not to cherry pick, I did search for studies reporting no association between SCFA's and MAP, and found none. I thought I'd bring this up because there is so much focus on short-chain fatty acids and GI health in general:
Isolation of lactate-utilizing butyrate-producing bacteria from human feces [...]
Short-chain fatty acids [...] are formed by microbial fermentation, and influence the health and function of the host colon (Cummings, 1981; Mortensen & Clausen, 1996). In particular, butyrate is the preferred energy source for epithelial cells of colonic mucosa (Mortensen & Clausen, 1996; Hagueet al., 1997), stimulates cell proliferation (Sakata, 1987), and promotes mucus release from colonic mucosa (Shimotoyodomeet al., 2000). In addition, butyrate has been implicated in providing protection against colonic cancer and colitis (Whiteheadet al., 1986; Scheppachet al., 1992, 1998; Segainet al., 2000; Perrinet al., 2001; Ruemmeleet al., 2003).

And this: Bowel Wars: Hydrogen Sulfide vs. Butyrate

The fuel for the bacteria producing SCFA's comes from Resistant Starches. This is interesting, as many of us try to avoid starch altogether (SCD, paleo, GAPS). Maybe that strategy should be altered, so that we limit the amount of regular starch in the diet, but include Resistant Starches (along with fiber)...
Last edited by a moderator:
In Germany, some doctors have been using butyrate enemas (can't remember its clinical trial/trademark? name right now) to treat ulcerative colitis.

The probiotic yeast S. Boulardii increases the amount of butyrate in the gut[1].

SCD restricts eating polysaccharides; but paleo has a wide spectrum ranging from very low carb (even ketogenic paleo) to high carb paleo... Paleo diet do not restrict eating polysaccharides, and most of the paleo websites I have seen endorse taking RS[2].
I think consuming RS is much more popular within the UC population than CD patients.

[2]:Sarah Ballantyne's warning is worth reading though: Resistant Starch: It’s Not All Sunshine and Roses
Last edited:

Deleted member 431298

2]:Sarah Ballantyne's warning is worth reading though: Resistant Starch: It’s Not All Sunshine and Roses
The main conclusion made by Sarah is that RS found in whole foods is beneficial, while the reducing RS foods may be why low-carbohydrate diets tend to alter the gut microbiome in unfavorable ways. It is only in one study where isolated supplemenation of RS (which cannot be generalized into other types of RS) resulted in a slightly higher DNA adduct, which can reflect oxidative stress. My point being: I think the title RS Not All Sunshine and Roses is too negative, and does not cover the topic very well.
Combining infliximab, anti-MAP and hyperbaric oxygen therapy for resistant fistulizing Crohn's disease

Lay abstract

Nine consecutive patients with Crohn's disease and fistulae were treated with a special combination of infliximab, numerous hyperbaric oxygen sessions and combined antibiotics including rifabutin, clofazimine and clarithromycin as the base antibiotic combination – called anti-Mycobacterium avium ss paratuberculosis (MAP) therapy. At between 6 weeks and 6 months all fistulae healed – included rectovaginal – so that the skin was dry and there was no discharge and no need to wear a pad. Their Crohn's symptoms of diarrhea, urgency and bleeding also resolved. Continuation with anti-MAP therapy alone maintained healing although one patient who ceased the anti-MAP therapy had a relapse.

This study was published in 2015 and it was posted in the Research subforum back then. I am posting it here so that more people can see it, especially for people who are dealing with fistulas. I think the study is remarkable.
Last edited:
An update. I'm past the 6 week mark since starting AMAT.

I have been having difficulties with the protocol. I've had an eye twitch for the past 3 weeks that won't go away no matter what I do, including magnesium. I've also been severely depressed and anxious, with bouts of fear and paranoia for no apparent reason. I thought it was maybe just the time of year but when I googled eye twitch and antibiotics, I was lead to many sites talking about the neurotoxicity of high dose clarithromycin that can cause these symptoms.

The improvements I mentioned earlier about my bowels were short lived. I'm back to bleeding and 5-6x daily BMs. They vary from 5-7 on the bristol scale. I've also started having upper GI pain that I've never had before in my life, including small intestine pain. I suspect that perhaps my bowel is being corroded by these drugs. Clarithro in particularly is *extremely* bitter. You have to take it with a full meal and even then it's hard on the body.

I fear that the abx are causing damage to my body. Some of the reports I read said that people had these symptoms even a year after stopping. I'm beginning to doubt this course of action. Even if it does kill MAP, what's the point if it also causes brain damage?

I'm taking 1000mg clarithro daily. I'm wondering if I should half that, even though AMAT research shows it to be ineffective at lower doses. The other problem is that sometimes the negative effects of clarithro don't kick in until weeks or months after you stop. While you're on them the body is in survival mode, putting everything it has into detoxing the abx... but once you stop it takes a rest and the true state of things is revealed.

Most MAP treatment protocols I've read say that improvements can start to be noticed as early as 1 month. For some people it's two months. It's weird how I had that brief period of 1 week with perfectly formed stool and no blood, to the point of constipation. Then it started to reverse again. Maybe that 1 week was the time of perfect equilibrium and now I am getting into imbalanced territory.

I am SO TIRED of playing guessing games with this disease. The only thing I can think to try is sending another blood sample to Otakaro to see if these 6 weeks have wiped out the majority of MAP. Though I don't see how that could be the case.

I also feel like whatever dysbiosis is being caused by the abx is a whole other level of body damage that's going to take me forever to heal. Last year I did a triple therapy for 10 days and it took about 2 months to start feeling normal.

I'm scared right now.

Deleted member 431298

Conner, that's not what I had hoped for you at all. I am very sorry to hear you are getting no improvement and nasty side effects. Also, I am a bit puzzled as to why the MAP resources have no testimonies that resemble yours. Some ideas as to why:

A) - you are the only one having these exact reactions, or maybe some concurrent infection just happened to hit you, like C difficile or something (that would be unlikely, would it not?).

B) - other patients who got side effects like you describe pressed on, found relief, and never been bothered to mention the hardships in their reports.

C) - those who get the serious side effects just quit to never look back and take the time to report what they experienced.

D) - ?? some other reason ?? (any thoughts?)

From memory, the side effects that are reported are different, typically transient problems with eye inflammation (not eye twitching though), skin tone change. Anyone heard other reports of the symptoms Conner lists? (Irishgal?)

The neural symptoms sounds like something to take very seriously, and I totally get your considerations about quitting the abx. It seems like your situation calls for some expert guidence...
I hope you will get better soon!
Yeah Ole - These don't seem like the normal AMAT side effects that I've heard of in talking to patients. (Huge disclaimer - I'm not a doc!!) The hard part is MAP may not really be implicated in UC, though I know of one patient who did amazingly on AMAT and had true UC. For the majority of true UC cases (which aren't misdiagnosed as Crohn's colitis) AMAT seems to work less or not at all.

Also, Connor seems to be extremely sensitive to antibiotics and meds. There are 10-15% of people per Dr. Chamberlin's anecdotal experience who just can't tolerate the meds. Some are allergic, and others just have a really hard time with them and have to stop. This is what's hard about not having a doc who is a MAP specialist to work with. There are so few docs who can adequately prescribe and adjust AMAT, and a lot of patients and docs are learning together.

There are other stories on forums and social media about AMAT not working for patients. None on HPF, but I've offered the option to a few patients who have interesting stories with this treatment, which ultimately failed. None have taken me up on my offer yet! I think Connor's story is either an anomaly specific to him, or maybe he has UC and the cause of his disease is not bacterial, or these meds aren't hitting at the specific bacteria. The fusobacterium varium research on UC is of interest to me, and it's a different regimen.

Regardless, I hope and pray Connor finds something which will work for him! ❤
There are 3 major variables here, actually 4.

1) Diet has been off lately, eating too much sugar (Christmas time)
2) Stopped prednisone just over a week ago.
3) Had an iron infusion 4 days ago.
4) My Entyvio dose is late by one week.

The anxiety/depression, I feel, is definitely abx related. I have not felt this way in a long time.

Deleted member 431298

I wish everyone reading and writing here a merry Christmas and a happy New Year.
One of the better christmas presents is good news from the MAP vaccine development. They report the phase I trial was a success (test for safety on healthy individuals). The development now moves to phase IIa which is testing on Crohn's patients.

Keep it up, folks!

‘The phase I trial was completed with no concerns over safety. As it was the first trial of this vaccine in people, a standard ‘3+3 dose escalation design’ was used to allow us to start with a very low dose for the first few volunteers and then gradually increase the dose once we were sure that there were no safety concerns.

All doses were well tolerated, immunogenicity looks very promising, and the study is now being written up for publication.

We would like to thank the healthy volunteers who took part in this phase I study without whom it is wouldn’t be possible to develop important new therapies.’

Phase IIa, a further safety trial, this time in Crohn’s patients, remains likely to start in the first quarter of 2018, and we will provide further details about this once they become available. The set up period in clinical trials is often unpredictable and as such we are unable to give an exact start date for the phase IIa trial at the present time. Please note that recruitment has not yet started, so we therefore ask our supporters not to contact us or St Thomas’ Hospital about this. ...

Deleted member 431298

There is an interesting comment by Dr. Greenstein and a colleague up on gastroendonews.com. The topic of the comment has been brought up previously in this thread but this new comment is well written and the argumentation rigorous, so I thought it was relevant to link to it:

To the Editor: More to the MAP Story

They reiterate the importance of acknowleding the anti-MAP effect of some of the usual CD drugs, in order to get valid results from past and on-going AMAT studies. Their primary concern is that the true effect of AMAT is hidden in studies, because the placebo-arm is inadvertently also recieving MAP-suppressing medicine:

[...multiple medications used in the therapy of inflammatory bowel disease cause dose-dependent inhibition of MAP in culture. These include 5-aminosalicylic acid (5-ASA),10 methotrexate,8 6-mercaptopurine (6-MP),8,11,12 azathioprine,11 cyclosporine A,9 rapamycin,9 tacrolimus,9 the 1-hydroxypiperidine-2,6-dione component of thalidomide (Thalomid, Celgene)5 and the thioamides (methimazole and thiourea).6

These medications are called “anti-inflammatories” and “immune-suppressants.” These appellations may be wrong. We suggest that they are describing a secondary physiologic response. We posit that their primary mechanism of action is as anti-MAP antibiotics...]
Last edited by a moderator:
I came down an enterovirus this week that landed me in the hospital. They ran a CT scan as a precaution and it showed that I have extensive small bowel inflammation. My stool tests are negative for c. diff and other obvious pathogens. Based on my recent history, it's likely that the antibiotics have been ravaging my gut. I have been taking probiotics this whole time but they obviously aren't helping.

On the advice of doctors and more importantly my own intuition, I've had to stop AMAT. My small bowel is in a lot of pain and my food absorption status is questionable. I've had to revert to taking morphine again.

The preliminary assumption is that the antibiotics have been corrosive to my bowel and productive of new inflammation. Once the enterovirus hit, everything exploded. My CRP in the hospital was 120 despite no signs in my colon. For the first 4 weeks of AMAT I was also on prednisone. In the last 2 weeks all the pain and discomfort I was experiencing were probably the previously masked side effects of the abx coming to light once my pred taper was complete.

It's interesting that at the beginning of December I had perfect stools and it seemed like everything was normal, but it then turned to constipation and renewed inflammation. I still cannot explain this anomaly.

The one thing I really need to say to the IBD / AMAT community at large that really is driving me crazy is that people need to STOP always calling symptoms "die off" when somebody complains about a set of symptoms. It's highly unlikely that you're having massive die off symptoms after a month of being on full dose AMAT. The majority of die off is going to happen in the initial stages as the active MAP + your gut flora are all dying. After that, "die off" events are more than likely something else, like your own native body tissue becoming inflamed, detox reactions from the antibiotics themselves, etc. When I told the ER doctors that I had been on Clarithromycin for 6 weeks they just shook their heads and said that it's a powerful antibiotic that is very harsh on the guts of most healthy people, let alone someone with IBD. I knew this going on, it's not news to me... but seeing the results in technicolour is another story!

I am glad I gave this a try. I'm upset that I probably still have MAP but have no real way to deal with it now. I wasn't able to stay on AMAT long enough to look for evidence that my IBD was improving with it. What I should have originally done was waited 6+ months for my flare damage to heal before trying AMAT. It may also just be that I can't handle long-term antibiotics like this.

The radiologist who examined my CT scan wrote in his report that I show Crohn's signs, but this should be re-assessed by a GI doctor. There are signs in the terminal ileum. The problem is that enteroviruses can also cause these signs so it's hard to distinguish. I will need follow up endoscopes. It's also possible that the antibiotics have been severely irritating to my gut but it was not possible to know due to simultaneously prednisone use.

I will come back to give an update once I have more information. I am super depressed that this treatment avenue has turned out this way. I feel like the answers are all still unclear. If I do indeed have Crohn's then it means my original diagnosis was wrong or my UC has progressed to Crohn's, which would fit with the MAP picture. Unfortunately now that I have stopped AMAT, future resistance to AMAT antibiotics is likely. FMT is really my last treatment avenue... after that, I have nothing left to throw at my UC. I've done it all.

Deleted member 431298

I am truly sorry to hear that you got so ill. IBD is just such a F..&%"¤% piece of ..¤%"&&# disease.
I probably mentioned this before, but Methotrexate (MTX) in a low dose (10-15mg/week) works well for me (with CD). It takes a month or maybe more for the full effect. Greenstein et al. found MTX to inhibit MAP in vitro.
I hope you will stick around and share your thoughts with us. Your observations regarding the "die off" term are relevant.