Submitted by Jim K on Sat, 2005-09-17 20:56

The Tunnel of IllnessI want to update my story on the front end so readers know even before reading the "agony post" how much benefit I've gotten from the treatment. It is August 26th, 2006. Coming up on two years I've been on the Combined Antibiotic Protocol (CAP) for Chlamydia pneumoniae (Cpn). A recent forum poster asked if anyone with CFS has improved on the CAP. My response:

Damned right I'm getting better!When I started the CAP I was in a 2 year slide after 25 years of CFS, then added FMS. For many years I'd struggled and somehow maintained a semblance of a life. Then over 2 years my pain, brain fog, restricted functioning, etc. slid to a point where I had to stop traveling and could for the first time see the possibility that I would become bedridden eventually.It has taken me two years, but the CAP has gotten me from the 10% functioning point to a 60% functioning point (I would say 70%, but I am superstitious to dare the gods too much). This is unbelievable, and as unheard of in CFS as recovering motor function is in MS. I have to say I turned a major corner sometime this spring-summer. I am now able to do two week Tini pulses which continuing to work, have had big improvements to energy and brain fog, and I have a sense of positive future I have not had for many years. From my discussions with Dr. Powell (my physician) and Dr. Stratton, I gather that I have another 2 years to go to clean it up entirely. I am happy to do so. My CAP reactions at this point have gone from grueling to merely unpleasant. I have undertaken remodeling my kitchen, a project of the kind which I have not been able to even conceive of for at least 5 years. That means I have sustained energy, motivation and followthrough. A bloody miracle. Give me another couple months, and I could go on...

  I've had CFS/FMS/MCS for about 20, long and tough years. For me it started with chronic fatigue, multiple chemical sensitivities, chronic Candida and other problems and has evolved into sleep disorder, bone deep fatigue, chronic dysbiosis, severe muscle pain & inflammation, brain fog, interstitial cystitis, frequent colds, etc. I can date the start of chemical sensitivities to flea treatment of my house with Dursban in 1974, a chemical now known by the EPA to create neurological, chemical sensitivities, and other chronic problems. I have dated the Candida to antibiotic treatment for chronic prostatitus around that same time. In retrospect I wonder if the prostatitis was the reservoir for Cpn that generated the chronic fatigue and fibromyalgia. By 1994 I had increasing inflammatory pain in muscles and joints, worsening sleep disorder and all the other stuff that typically goes along with Fibromyalgia. I have gone through a ton of treatments, supplements, and detox programs over the years seeking help. The only things which have sustained me and made a physical and functional difference have been energy work, tai chi and, for a time, EPD (Enzyme Potentiated Desensitization) and stimulants. Somehow, despite profound fatigue, I’ve continued to work, written a couple books, and had a family, keeping myself moving through this continually narrowing “tunnel of illness.” The latter is the phrase I use which best characterizes the experience of illness: how it narrows ones focus in life, closing off one thing after another until, eventually, all one can attend to is whatever light one can see to move forward towards. When that light occludes, all hope is lost.Over the last two years my fatigue, pain levels, brain fog began to get worse and worse. I travel overseas a lot for my work, and by Spring of 2004 I was in such bad shape I knew I couldn’t travel any more. I would arrive barely functional mentally and physically for my work. I could pull myself together enough for by narrowing my focus even further to push through the constant inflammation, pain and fatigue and massive brain fog: but the cost was that I had nothing left for myself, my family or anything that makes for a life worthwhile. The walls of the tunnel had closed in and the light was occluding.In a renewed and desperate search, saw an ad in the newspaper for a new Fibromyalgia and Fatigue Clinic in town, which had a broad-based integrated-medicine approach. I started with them in August 2004. Among other things, they tested for a large panel of occult infections (viral and bacterial). Cpn (Chlamydia pneumoniae) came up high on the antigen tests (both IGG and IGA). The doctor there started me on three months of tetracycline in September 2004. Within 3 days I had a severe endotoxin reaction (sometimes, inaccurately, called a “herx”). Shorthand: severe pain in every part of my body, utterly flattened by fatigue, extreme irritability and depression, discoordination, (these last two were likely secondary porphyria reactions), etc. These reactions went on for the rest of that first week, then tapered to a lower, manageable level of the same. Over the three months on tetracycline the biggest change was that my overall inflammatory pain levels lessened noticeably. For the first time in a couple of years I could stop my constant use of ibuprophen. However, changes in my overall fatigue and brain fog did not lessen. By this time I was also starting on a bunch of supplements, thyroid T3 and immune boosters from the Clinic in response to other blood results.True to form, incessant (my wife & kids would say ”obsessive”) researcher that I am, I took to the web, to search about Chlamydia pneumoniae and found David Wheldon's regime. His reasoning and evidence made sense to me as to why I might not be feeling better despite the tetracycline, and helped me to appreciate the difficulty of eradicating this organism. I ran the Wheldon protocol past my CFS doc, who fortunately was very willing to prescribe the Doxycycline, Zithromax and Flagyl. This was December 2004. The switch to doxycycline was no problem. The addition of Zithromax gave me another round of “herx.” It was apparent that the Zithromax was killing more Cpn and seemed to reach deeper into some tissues than the doxy alone, especially muscle and connective tissue in my upper back, sacral area, neck and trapezius. Wheldon and Stratton have both noted that, despite these antibiotics being understood mostly as being bacteriastatic (interfere with replication), in combination they can have some bacteriacidal effect (kill bacteria outright).I did not dare try to add Flagyl until mid January 2005, and then only one 500mg dose. With this one dose, for the first time in years, I felt a brief lifting of some deeper fatigue, as if a weight I had been dragging was lightened just a bit. I was so enthused by this sign that, of course, I laid a plan that got me into trouble. Anything worth doing is worth overdoing, right? If some is good, then more is better… right?I could only tolerate one 500mg dose of Flagyl at first. With a second dose I felt very nauseous, and sick all over. But, I also felt improved for a couple days after. Then, despite the continued doxy/zith combo, I would slide back quickly into the usual fatigue, brain fog and body aches. So, I decided to do one dose of Flagyl once a week for a couple weeks, and worked that up to 2 doses (one per day) once a week, then 2 doses each day for two days. Then 2 doses for three days weekly. You can probably see where this is heading.While initially this seemed to leave me feeling better, by the time I worked up to three days of Flagyl once a week two things were happening. One is that I seemed to be getting more sensitized to the Flagyl itself, and began to get terribly nauseous and sick from even the first dose. No build up needed. I thought a drug reaction or a conditioned reaction, but if you read the Expert Comments of Dr. A., it could well have been increasing bacteriacidal reaction of the cryptic form of Cpn (i.e. to the die-off). Second, as David Wheldon has noted, reactions to the Flagyl pulses can go on for days, even weeks probably because the immune cells (lymphocytes, monocytes and macrophages) which get cleared of Cpn start doing their jobs again. Then you get a “herx” from your own immune cells killing the Cpn and the usual resulting endotoxin and cytokine reaction. (See article) There is also evidence that the bacterial envelopes that contain the endotoxins remain behind for up to 4 weeks in infected tissues, even when the bacteria are killed, i.e. leaving inflammation behind. (See article in our Research Articles section).I finally came to my senses— I was doing too much, too fast. This is a recognized hazard of anyone who has been sick for a long time and is starting to feel better, or even hopeful: if a little is good, more must be better. So I did two things. I asked my Doc to switch me to Tinidazole, which David Wheldon had said some patients tolerate better than Flagyl, and I followed the every-three-weeks pulse rules of David’s protocol, giving my body time to catch up to the impact. With the Tini I have been able to build up to a full dosage (500mg three times per day) for the full five-day pulse. However, I confess to continued zeal (read “glutton for punishment?”). Having talked to another Cpn patient who was using the current Vanderbilt protocol, I decided to add amoxicillin because of it’s putative effect on the Elementary Body (EB) stage of Cpn. Having just experienced feeling improved during and after my Tinidazole pulses, the addition of amoxicillin now gave me back renewed pain and inflammation! You’d think I’d leave improvement alone for a bit. Now I had, again, severe pain in my ankle joints, back, illeo-sacral, trapezius area (all of these had been loci of on-going pain in the past but had calmed down on the first months of tetracycline, and continuing doxy/zith). Plus, something that had not yet improved now got even worse: brain-fog and fatigue. The good news? I guess now I know where the Elementary Bodies are harboring: in my joint and muscle tissue. I’ve slowed down on my addition of amoxicillin, and can now tolerate one dose a day (500mg). I’m not in any hurry to add the second dose. Just the last day or so, I even seem to be having diminishing pain and more energy. I’m no poster child yet for cure of Chronic Fatigue with the Cpn protocol. Maybe I can be the poster child for Can’t-Quit-While-He’s-Ahead? At least I can be a role model for how not to do it! And I certainly don’t have any enthusiasm to add Rifamcin any time soon—until I’m sure my total load is down.It seems to me that having CFS for this long I’ve probably built up a tremendous load of Cpn, in all of it’s life phases, in a variety of tissues. If I had had central nervous system infection I’d probably be dead by now. That the locus of infection is muscular, connective tissue, joints and intestinal I have been able to store lots of the organism and still function. I’m not sure if this is good news or bad news, since I’m still amidst it. But, as Dr. A. said in the interview, “My generalization is that: the longer the person’s been sick and the sicker the person has been, the more problematic the therapy is going to be.”Current protocol (as of 9/17/05):100mg Doxycycline twice a day500 mg Zithromax every other day500 mg Amoxicillin once a day500 mg Tinidazole, three times a day every three weeksSupplements:Buffered Vitamin C powder (Allergy Research Group) during Tinidazole pulses when get endotoxic but doesn’t seem as effective for the Amoxicillin die-off.400mg CoQ10 gel cap once per day1 cap Fish Oils (720mg) three times a day1 cap 1000 units Cholcalciferol twice a day1000mg B12 two to three times a day (or equivalent methylcobolamin)2 caps NK Stim (olive leaf, larch extract & aloe powder) twice a day4-6 Caps Life Force Multi Vitamin per day1000mg Evening Primrose Oil twice per day1 cap Quercetin with Bromelain, three times a day- took this for anti-inflammatory effect on urinary system, but turns out it's also antichlamydial. 1 cap pregnenelone plus DHEA once a day- these levels are low in my blood tests. DHEA appears to be used up in endotoxin detoxification (see article). Other meds:60mg Cymbalta (for pain and mood)Ambien & Klonopin for sleepIbuprophen as needed for pain/inflammationAdderall for brain fog. Trying Provigal for this lately, which I reacted to poorly previously, but seems to be more useful now in keeping me alert without the stimulation of the Adderall—I think this may be working better because my bacterial/endotoxin load is coming down enough to make a difference! Current status?As of 9/15/05, about 10 months into a Cpn protocol, what’s improved?I would say that overall my improvement is slow, steady and gradual, with ups and downs. My close friends note that, despite down periods; they see a marked improvement between how I was a year ago and now. More specifically:Pain and inflammation- significantly improved (except when adding new antibiotics or during Tinidazole pulses)Constant colds & infections- appear not to get colds any more often than “normal” folks, despite a job with regular people-contact.Fatigue- has improved only slightlyBrain fog- only brief improvements, mostly during Tinidazole pulses.Sleep disorder- no improvementExercise tolerance (improved until I added amoxicillin, now worse until I get through the inflammatory cycle)Interstitial cystitis- improves during Tinidazole pulses, worsens again between pulses, but better overall than it was.NK cell levels- now normal range!IG levels- still below normal (I’m getting checked out by immunologist for this soon)Cholesterol- Significantly improved. LDL’s dropped, ratio back to low risk. I attribute this to fish oils combined with the lessened endotoxin demands on cholesterol for detoxing (see article in our Research Section).As for the tunnel of illness? The walls are widening, I can see the light ahead once again, and the world beyond the tunnel is almost imaginable at times. About to travel overseas. First time in year, so it may be the big test at what recovery I have. I’ll keep you posted,JimK

Update 2/6/2006

I've posted this in my blog, and thought it would be a good addendum update to my story. I'll add more detail here on current protocol. In an email to me, one of our new members noted how long I'd been on the protocol and asked me if I'd improved on it. It was a legitimate question, and one that on a day to day basis is not always clear to me, since I continue to have symptoms, and the slope of my improvement has been very gradual. As has been said elsewhere on this site by experts, the longer you've had Cpn, the more systems involved, the higher the bacterial loadi and so on, the longer and more arduous is the treatment. My CFS diagnosis means that it's been a chronic condition- underline the C in FS. So I wanted to report my assessment of this based on some recent experience.Yes, the protocol has indeed helped. I've had this bug seriously (undiagnosed) for at least 20 years, so my tissue loadi was very high to begin with, and I had to go very gradually to get at it. As you can read in my Patient Story, I was not feeling very patient about the whole thing, wanting to push up doses too fast, suffering more because of that, and so on.  The longer you have had it, the harder to treat, the more reactions to treatment, etc. Certainly so for me. And the slope on the curve of improvement is also very low in such cases. I've reported other changes in my Patient Story and in previous blogs, but had a very clear reference point recently as to how much I've improved. I travel and teach workshops overseas. By Spring 2004 I could no longer tolerate the travel and feel I could deliver quality teaching. I stopped traveling for a year and started treatment in fall of 2004. I went back overseas to Europe again for the first time in September 2005 and found that, while quite tiring and my recovery to the time change was hard, I could function adequately. It was still tough, though, and took a lot out of me. Now, having done another trip to Europe in January 2006, I could see a clear difference in my resiliency: faster recovery from the travel fatigue, easier and faster adjustment to the time change, and my level of functionality while there teaching was significantly improved. My recovery has been such a gradual slope over time, that I don't think I would have credited it as clearly just staying at home, without these identical "big challenge" events to compare. And the only difference in terms of variables was 3 more months of treatment. Of course, I have had gradual improvements all through treatment, especially noticeable after the first couple of full tinidazolei pulses in particular (which it took me about 4 months of building up the abxii treatment to tolerate, and at least 4 mini-pulses). Stratton has said this is a 1-3 year treatment, depending on your response. Given my slow course I'm expecting the longer side of this. I have recently added INHi under Dr. Powell, and so I expect some things to improve a bit faster after I get used to the additional die-off. We'll see. But there is no doubt in my mind that this treatment has not only saved my life, but given me life back. It's just that now I'm greedy for even more!Greedily yours,Jim

Protocol as of 2/6/2006:

  • 100mg Doxycycline twice a day
  • 500 mg Zithromax every other day
  • 600 mg NAC twice a day
  • 500 mg Tinidazole, twice times a day every two weeks
  • 150mg INH working up to 300mg 


  • Injectable B12 2mg two-three times per week.
  • Injectable Mg 2mg three times per week 
  • Buffered Vitamin C powder (Allergy Research Group) during Tinidazole pulses when get endotoxic but doesn’t seem as effective for the Amoxicillin die-off.
  • 400mg CoQ10 gel cap once per day
  • 1 cap Fish Oils (720mg) three times a day
  • 1 cap 10,000 units Cholcalciferol once/twice per week depending on blood levels
  • 5000mg B12 two to three times a day
  • 2 caps NK Stim (olive leaf, larch extract & aloe powder) twice a day
  • 4-6 Caps Life Force Multi Vitamin per day
  • 1000mg Evening Primrose Oil twice per day
  • 500mg Niaspan (working up to 1000mg) with 800 units Vit E
  • 200mcg Selenium 
  • 400mg chelated Magnesium twice a day. 
  • 1 cap Quercetin with Bromelain, three times a day- took this for anti-inflammatory effect on urinary system, but turns out it's also antichlamydial.
  • 1 cap pregnenelone plus DHEA twice per week- these levels are low in my blood tests. DHEA appears to be used up in endotoxin detoxification (see article).

Anti-Endotoxin herbs:

garlic, ashagawanda, ginseng, horny goat week: 2 cas each 2-3x per day

Other meds:

  • 30-60mg Cymbalta (for pain and mood)
  • Ambien & Klonopin for sleep
  • Ibuprophen as needed for pain/inflammation
  • Adderall for brain fog. Trying Provigal for this lately, which I reacted to poorly previously, but seems to be more useful now in keeping me alert without the stimulation of the Adderall—I think this may be working better because my bacterial/endotoxin load is coming down enough to make a difference!



Update on my protocol:    I've been up to twice a day amoxi for about 1 week now. Various old places flair up and then clear as the EB load is killed and different tissues are reached: sacroiliac, lumbar, trapezius area, left wrist felt arthritic, hands hurt, then left knee, ankle and foot along with right knee. Fascinating (now that it's not so horridly painful) to watch the sequence and recognize places I've had complaints or pain over the years show themselves. Today on my 3rd day of Tinidazole pulse, my 9th "pulse" of the azole drugs, but only the last three including this one have been full 5 day courses. It has brought aches, knee swelling, fluey feeling, but much less than ever before, and I can think better, though my eyes burn like crazy. Still not eager to get onto the rifamcin, but grateful I added the amoxi which, given the CFS/FMS symptomology, I am realizing that so much of my chronic pain and fog has been EB's loading up in the tissue.On Wheldon/Stratton protocol for Cpn in CFS/FMS since December 2004.

Jim, I am not surprized that you are not eager to touch rifampin. I am scared of it, too. It is out of topic and I can't find this report now, but I found out that it Amoxicillin is capable of crossing the BBB in dose of 6 gm a day. Some people eradicated Borrelia burgdorferi this way.

Cured of multiple sclerosis, stopped the Wheldon's protocol in Nov,2008. Use only LDN.

Hi, I am curious about the eye burning...?  Is this an endotoxic reaction to the ax treatment?  I just finished a round of azith. for a sinus infection and my eyes are still burning.

Wheldon Protocol for rrms since Oct '05.  Added LDN 4.5mg qhs Oct '07.  All supp's.  Positive IGG's for Lyme Disease,Babesia, & Erlichiosis Sept. 2008.  Currently:  Mepron 750mg bid and Azithromycin 250mg qd for Babesia.

Burning eyes definitely endotoxin/cytokine reaction. Always got worse with abx. Seems to be lessening as the EB population diminishes and the total bacterial load comes down, and worsens when I add something new to the protocol or start a Tinidazole pulse. I'll start a forum on listing one's abx reactions and we can all sort this out together. On Wheldon/Stratton protocol for Cpn in CFS/FMS since December 2004.

I have had CFS for almost 8 years now.  I'm 29 but feel like 90.  Your story gives me soooo much hope.  I have been praying for 8 years for God to heal me and he has shown me the way to healing.When I became ill I was a pre-med student.  Medicine is what I love.  I have had my horrible experiences with narrow minded drs like I'm sure everyone here.  I do have hope now that I will be able to go to medical school one day now.  Before it was unthinkable and now it seems possible.  I also know what kind of dr I want to be and what my specialty will be.  I want to specialize in CFS/ME, FMS and all those mystery illnesses and of course focus on Cpn!!!I believe that God has allowed me to go through all this for a reason!!!Gisela

CFS and IBS/Candidiasis since 2000, 100mg once daily doxy since 8/21/08, 250mg azithro MWF since 10/3/08, flagyl pulses, vit D3

being realistic, it sounds more like research on your part, and scientific knowledge has had much more to do with you finding a potential cure... rather than talking to an imaginary man in the sky.You might do better to get into the science and facts, rather than your superstions if you're serious about getting better.Best of luck mate 

Hey Ben,  Might be well to take a look at the date of the post that your are responding to if you really expect answers.   By the way are you in treatment with CAP?  Or perhaps considering it for yourself?   Or what?Best of luck to you whatever,Louise

  • CAP(TiniOnly): 06/07-02/09 for CFS
  • MethylationProtocolSupplements: Started08/08
  • Intermtnt CAP: 02/09-02/10
  • Full MethylProtocol & LDN 02/09
  • Off CAP: 02/10, cont LDN & MethlyProtocol support

Jim Thank You...Mr. K thank you for sharing your battle with your health...I felt as I was reading what you wrote as if I had written so much of it..I know many others have hadto struggle with these same physical challenges........I  have struggled with this for 13 years...Been to so many doctors with so many different opinions..For the most part no real clear idea what was the illness...For so long truly thought it was mental at times...Have been able to work for all but a short period of timewhen the doctors thought I had Parkinson's and was on meds that cause serious side effects that cause the syptoms to get worse thus not able to work safely..I am currently see the Doctor at Fibro and Fatigue center...She shared this web site with me..This site has given me so much information that I can better understandand when I can not understand the first time reread it after having read something elseyou have posted been able to go back and understand a little more...Thank you , Thank you , Thank you for all of the time you put into this and my hopes areyou are Truly on the Road to Recovery in this war we are personally fighting...Jon 

I'm very grateful that this is of help, Jon. Your comment makes me feel less alone as well. We are creating a community of support here, and each person posting makes it more powerful. Now all we have to do is change the medical establishment! On Wheldon/Stratton protocol for Cpn in CFS/FMS since December 2004.

Changing the medical professions views can and most likely is more difficult than getting rid of the cpn... not that I am a pessimist, I do hope that we can make a little change with a few doctors that are willing to try different thingsto help us... I am having some difficulty digesting all of this information ,, recallingit is an even bigger challenge..I am working on it though..Very very sceptical that I will ever truly recover from this illness...At least knowing what is going onand being able to say with black and white results that this is my problem is more than what I have been able to say for the last 13 years is a step in understanding and accepting what is ...

You are helping your self and helping many others and that is the best anyone can do.  I just got the table you did comparing protocols and I have read many posts you write to help every visitor.  I hope you realize that you are doing lots of good so please keep up this outstanding job!Yes, I am cheering you so you can keep cheering all of us!!! And because I see you are doing so many amazing things in this site, well, I do not mean to overload the list of work but... as a newcomer I find very difficult to follow up specially when you all use so many short words:  abx, cpn, mms, protocol, etc etc.. would be very good to have a list of common a dictionary?  sorry if it means more work! God bless you!Maria P.  

God bless you all.MariaPatri - living in a rollercoaster! (In Orlando, Fl).Thyroiditis, sinus infection, heart, muscles and joints. 

Jim, thank you for posting this ..... with so many new people coming on board, I've been feeling  as if we needed to instill perhaps a "status rally" from some of the older members. Your posting this is very inspiring to those of us with CFS and FM.  I'm 1 year and 4 months in and just did my 3rd pulse...(not even up to the full ones yet) -- I can pretty much relate to all you described... this has not been a fun ride, but the light at the end of my tunnel is getting brighter.  I am getting better! Be well,Jeanneroz  

JeanneRoz ~ DX'd w/ CPN 4/2007; 6/07 -"officially" dx'd w/CFIDS/FM; also: HHV6, EBV, IBS-C, 100 Doxy:BID; 500 mg Biaxin BID; Tindamax Pulses, B12 shots, ERFA Dessicated Thyroid,Cortef, Iodoral 25 mg, Vit D-6,000 uni

Hi Jim You said the following  "I had a severe endotoxini reaction (sometimes, inaccurately, called a “herx”). "Can you explain the difference?