Up from the Ashes: James’s Severe ME/CFS Recovery/Recovering Story

by Cort Johnson | Jun 15, 2022 | Abilify, Cytokines, Diagnosis, Drugs, Homepage, Hydrocortisone (Cortef), Immune, Mast cell activation syndrome, Mast cell activation syndrome, Recovery stories, Severe ME/CFS | 288 comments

I’d been corresponding with Frank, James’s father, for several years. His son, a former emergency room doctor, had a very severe case of ME/CFS, and Frank had been beating the bushes to find anything that could help. Nothing, however, was working. Recently, though, I got a surprising message. His son was on the mend. Below is a rare story – someone with a very severe case of ME/CFS – who has made remarkable progress.

Prior to getting ill, James worked as a professional model to put himself through medical school.

My illness started in 2009 at the end of my Residency medical training as an emergency room doctor. I worked as a California Board Certified E.R. Doctor before I collapsed at work in 2015 and ended up bedridden and incapacitated.

Prior to becoming ill, I was in excellent shape. Pre-med school, I worked 50 hours a week training clients as a fitness trainer. My own personal activities included hitting the gym, alpine and cross country skiing, long mountain hikes, beach jogs and swims, rollerblading, and mountain biking. I helped pay my way through medical school as a professional model. I was the picture of health. Nobody, including me, would have ever thought that I, of all people, could ever have become so ill.

I can identify with what Whitney Dafoe and others are going through on a very real and deep human level: I was mostly bedbound for almost 6 years, clinically declining all the time, wearing earplugs constantly to block all sounds and a black T-shirt over my eyes because I could not tolerate light or visual stimulation. I could only wear shorts because my body was so painful to touch/pressure. I could only whisper to my mom that I was “dying,” and I used hand gestures for things I needed.

If I pushed myself too much during the day, I would enter a state I called my “energy crashes.” I attempted to explain through scribbling to my mom that this was known as post-exertional malaise and it would take me at least 2 to 3 days to recover. Living within such an extremely limited envelope of energy and functionality was beyond challenging and overwhelming — it was pure suffering.

I endured massive digestive issues, food and chemical sensitivities, and many other symptoms including fatigue, weakness, aches, muscle cramps, joint pain, unusual pain, ice pick pain, headache, red eyes, blurred vision, tearing, sinus problems, cough, shortness of breath, abdominal pain, diarrhea, morning stiffness, memory, focus, concentration, word-finding issues and confusion, disorientation, skin sensitivity, mood swings, sweats (esp. night sweats), temperature regulation problems, excessive thirst, static shocks, numbness and tingling, vertigo, metallic taste, and tremors. At the age of 43, my formerly brown hair started turning gray and white. I dropped from a fit 220lbs to 149lbs. My mother’s living room became a makeshift hospital.

Despite seeing dozens of doctors, including some ME/CFS experts, for six years, the former fitness buff and emergency room doctor kept declining. Eventually, he became completely bedbound and could not speak.

Thinking was such a huge issue. I had to apply my meditation techniques and just focus on my breath throughout the day and night just to slow my mind down and conserve energy. My breathing techniques were also a small escape from the sick feeling I experienced constantly.

Over time, I have visited with over 42 physicians, including 2 affiliated with Stanford, who specialized in CFS/complex diseases. I have undergone every sophisticated test in the world: my blood was sent to Germany; I’ve had surgical procedures; stellate ganglion blocks; IVs; central lines; ketamine injections; MRIs of the brain and CTs of the body; numerous trial medications (Abilify, hydrocortisone, and others), many supplements and IVs. The list goes on and on.

Either the treatments made me worse or had no effect.. Attempts to treat inflammation with Abilify, or my extremely low cortisol levels with hydrocortisone, for instance, made me worse. No etiology of my “root” problem was ever found. All I was left with was the term “ME/CFS” – a term, it ended up, that helped me not at all.

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I needed a totally new approach to my health. Thankfully, I found it and that made all the difference.

My Breakthrough

Everything changed after I did something called the GENIE (Genomic Expression: Inflammation Explained) test while under Dr. Heyman’s care, and obtained a diagnosis of having the biotoxin illness also known as CIRS (Chronic Inflammatory Response Syndrome). CIRS is a multisystem and multi-symptom neuro-endocrine-metabolic-immune disease process.

Dr. Heyman

James finally found help with Dr. Heyman (From YouTube recording of a Japanese conference).

I found out about Dr. Andrew Heyman from a friend who heard a podcast on a medical breakthrough regarding the GENIE test. Dr. Heyman, who is triple board-certified in Family Medicine, Integrative Medicine and Anti-Aging and Regenerative Medicine, is the Medical Director of Integrative Medicine at George Washington University.

He is also currently the Chief Medical Officer and co-founder of the Metabolic Code, the Director of Academic Affairs for the American Academy of Anti-Aging Medicine, and oversees the training of 1000s of medical professionals. He has several leadership positions in the Integrative Health field. At the University of Michigan School of Public Health, he was responsible for administering a $7 million NIH grant to research alternative therapies for cardiovascular diseases.

He’s worked with Dr. Ritchie Shoemaker – the creator of the GENIE Test – for the last 16+ years. (Dr. Shoemaker technically is not practicing anymore. Check out his Surviving Mold website)

Dr. Heyman is often the LAST STOP for patients with mysterious illnesses. In my experience, he spends much of his time cleaning up other doctors’ messes and misdiagnoses of patients with ME/CFS, etc. (I believe the sun will be setting on this term soon enough as more doctors are becoming aware and literate with GENIE test).

The Masquerader: Chronic Inflammatory Response Syndrome (CIRS)

James believes CIRS masquerades as many illnesses. He writes: “Patients with CIRS are often misdiagnosed as having depression, anxiety, post-traumatic stress disorder, and somatization; as well as Alzheimer’s, Parkinsonism, allergy, fibromyalgia, autoimmune disorders, and chronic fatigue syndrome (ME/CFS), among others. Similar gene expression patterns were recently found in long COVID. Treating patients for these seemingly diverse conditions does not improve their symptoms of CIRS, although effective therapies for CIRS exist.”

“The reason this illness is frequently misdiagnosed is because health care providers are not aware of tests that can identify CIRS. With proper detection, diagnosis, and documentation of the objective basis of illness pathophysiology, CIRS may be treated effectively to improve symptoms and decrease the recurrence of uncontrolled inflammatory responses.”

“CIRS WDB is CIRS developed after chronic exposure to the interior of water-damaged buildings typified by resident microbial growth, including bacteria, filamentous fungi (molds), mycobacteria, and actinomycetes, together with resultant biologically produced toxins and inflammagens.”

“Since CIRS constitutes an activation of the innate immune system, which does not show up in most laboratory tests, making a proper diagnosis is difficult. Several biomarkers have been identified and there is a genetic component that can be tested. Low levels of a hormone, vasoactive intestinal peptide (VIP) that regulates smooth muscle functioning among others, and melanocyte-stimulating hormone (MSH), and high levels of TGF-B1 and complement factor4 (C4a) are often found. Several others (AGA IgA/IgG, ACTH/Cortisol, VEGF, ACLA IgA/IgG/IgM, ADH/Osmolality, MMP-9, leptin) are assessed as well.”

“CIRS is essentially a brain on fire. A dominant clinical feature of CIRS concerns cognitive complaints including memory loss, as well as mood disorders, brain fog, loss of executive function, and fatigue. CIRS is diagnosed using multiple markers that measure the innate response and the presence of inflammation in the brain.”

“There are now over 1,700 research papers to date on CIRS/biotoxin illness, but most mainstream doctors are not trained or lack experience in this field. (I wish I was armed with this info during my medical residency.) The good news is that this information is now being funneled into mainstream medicine and being taught in Residency programs.”

The GENIE Test

It was Dr. Ritchie Shoemaker’s GENIE (Genomic Expression: Inflammation Explained) which proved to be the medical breakthrough that allowed James to find relief after seeing dozens of doctors and taking every test under the sun. The GENIE test, it should be noted, is NOT just for mold; it’s designed for diagnosing a chronic fatiguing illness.

Shoemaker reported that the test, which was based on the work of James Ryan, Ph.D., took three years to develop and validate. The test assesses gene expression to determine if hypometabolism (low metabolic activity) – a frequent finding in ME/CFS metabolomic study results – is present.

The hypometabolism panel contains 175 reporter genes and covers the expression of everything from mitochondrial ATP synthase to Toll-like receptors to caspases (apoptosis).

Shoemaker reports that the GENIE test will show if a person has CIRS, if they are recovering, what parts of the body to focus on, if they are in a relapse. As the patient recovers, the test should show that the genes that were turned off are becoming activated again.

The test is called “research use only” which means that doctors must order the test; patients can’t do that yet. (Shoemaker state’s they are in the process of making that happen.)

The Visual Contrast Sensitivity (VCS) Test

Dr. Shoemaker reports that biotoxins and the inflammatory response they produce reduces the velocity of the flow of red blood cells reaching the eye. This causes problems sending visual information through the optic nerve to the brain and results in a reduction in CIRS patients’ ability to detect visual patterns. During a VCS test, the patient is shown a series of images specifically created to measure the person’s ability to detect visual patterns. Shoemaker reports that the VCS test positively diagnoses 98.5% of CIRS cases. The VCS test is performed at the initial visit and is repeated at each visit thereafter to assess progress.

James was too ill when he started the protocol to do the VCS test and so never formed a baseline. He is going to do the VCS test when he finishes the protocol.

Find out more about the test here.

James’s Test Results

James reported that his GENIE test results showed CIRS, stage 2, caused, in part, by toxins produced by actinomycetes bacteria. Actinomycetes bacteria are commonly associated with water leaks in the home and produce exotoxins that can cause symptoms like fever, chills, and respiratory problems.

Despite the fact that Shoemaker has largely been identified in the public with mold, he reports that forty-two percent of patients have actinomycetes bacteria while less than 10% are found to have the toxins produced by mold (mycotoxins). The remainder of the patients typically harbor fragments of a microorganism or biotoxins.

James noted that biotoxins are biologically produced toxins that can trigger a chronic, systemic inflammatory response in people who are susceptible to them. Approximately 25% of people have HLA (human leukocyte antigen) genes that impair their body’s ability to eliminate these toxins. These are the people, Shoemaker and Heyman assert, that are most likely to develop CIRS.

A nasal swab kit from MicrobiologyDx found a 3+ thick biofilm of MARCoNS (Multiple Antibiotic Resistant Coagulase Negative Staphylococci) in James’ nasal passages. According to Dr. Heyman MARCoNS is an antibiotic-resistant staphylococcus bacteria that resides deep in the nasal passage of about 80% of people who have low MSH (melanocyte-stimulating hormone) levels. Most of these people suffer from biotoxin illness and other chronic inflammatory illnesses (CIRS).

A laboratory-produced biofilm. Dr. Shoemarker states that when found deep in the nasal passages, MARCoNS bacteria can produce treatment-resistant biofilms. (From Wikimedia Commons.)

MARCoNS is not an unusual pathogen – almost everyone carries it in their nose. In fact, MARCoNS is usually thought of as a commensal bacteria; i.e. it’s part of our normal flora. It’s when MARCoNS gets down deep in the nasal passages that Heyman and Shoemaker and some other functional doctors believe the trouble begins.

Because melanocyte-stimulating hormone (MSH) protects the deep mucous membranes in the nose from MARCoNS colonization, Shoemaker and Heyman believe low MSH levels often precede the development of CIRS. Exposure to mold, chronic Lyme disease, and biotoxin illnesses can all deplete MSH, allowing the MARCoNS bacteria to colonize the deep nasal passages.

The Gist

A former fitness trainer, fitness model, and emergency room doctor James hardly seemed the kind of person headed for about as severe a case of ME/CFS as you can get.
Over a period of six years though – despite seeing numerous doctors including ME/CFS experts – James’ health continued to decline and decline – and eventually, he became bedbound, and was unable to speak, tolerate light, sounds, or touch. His brown hair turned gray and white and he lost 70 pounds.
After taking the GENIE test developed by Dr. Shoemaker while under Dr. Heyman’s care, James was diagnosed with a stage 2 chronic inflammatory response syndrome (CIRS) illness – otherwise known as a biotoxin illness.
Dr. Shoemaker and Dr. Heyman believe that many people diagnosed with ME/CFS as well as neurological illnesses and others actually have CIRS – the roots of which often begin with low melanocyte-stimulating-hormone (MSH) which fails to protect the deep nasal passages from biofilm enhanced bacterial infection that drives the illness.
Since few practitioners assess the activation of the innate immune system the immune ramifications of the illness are often missed.
The GENIE results suggested that James’ main problem was not mold but increased levels of actinomycetes bacteria, the presence of a treatment-resistant biofilm of MARCoNS (Multiple Antibiotic Resistant Coagulase Negative Staphylococci) in his nasal passages, low melanocyte-stimulating hormone (MSH), hypometabolism, hypercoagulation of the blood, increased expression of the Ikaros and histamine genes, among others.
James began Dr. Shoemaker’s 12-step protocol under the care of Dr. Heyman who supplemented the protocol with treatments to improve his damaged gut. (See the blog).
Since he started the protocol 16 months ago, James reported “I’ve had slow but steady progress since I started the treatment protocol. At the time I was almost literally on my deathbed.” While he cannot exercise yet, he is able to engage in most of the activities of normal life.
Not surprisingly James is a strong proponent of the CIRS approach and suggests that everyone ask themselves if they are on the right path – and consider checking out CIRS if the answer is no.
James plans to return to the medical field once he fully recovers and become a biotoxin/CIRS specialist.
Take the CIRS symptom diagnosis poll at the end of the blog to see if you might have CIRS according to Dr. Shoemaker. Also, if you have tried the CIRS protocol please tell us how it went in the poll.
If you’d like to communicate with James please leave your email in Health Rising’s Contact form and I will pass it on.

Once in the deep nasal passages MARCoNS wraps itself in biofilms – making it especially difficult to treat – and creates exotoxins that activate the immune system. MARCoNS also produces a substance called hemolysin that breaks up MSH, further inhibiting it, and which can increase cytokine levels and inhibit the functioning of T-reg cells.Plus, low MSH produces hormone imbalances, mood swings, leaky gut, alternating constipation and diarrhea, lower melatonin levels (poor sleep), and low ADH (antidiuretic hormone).

The end result, Shoemaker believes, are the familiar symptoms (body aches, debilitating exhaustion, etc. found in people diagnosed with ME/CFS and similar diseases.

James’s GENIE test also confirmed severe molecular hypometabolism, high rates of apoptosis (cell suicide), a hypercoagulable state that was likely causing nerve damage, and increased expression of the Ikaros gene. Shoemaker reports that an altered expression of this gene is found in 85% of CIRS patients with hypersensitivities to environmental chemicals, drugs, supplements, and foods. Shoemaker appears to be the first person to attempt to get at the molecular roots of this knotty and very mysterious problem. If he’s right, that would be something indeed.

James’ gene expression test results also cleared up another mysterious problem. While being seen at Stanford, he was diagnosed with having mast cell activation syndrome (MCAS) and prescribed multiple courses of antihistamines – which he reacted poorly to. The GENIE test indicated a possible reason why – – a gene involved in histamine production was overly expressed and had a polymorphism (small mutation) that impaired its functioning as well.

Interestingly, James’s test did not indicate that he had a problem with mold or a genetic susceptibility to it. Some doctors report that about a quarter of the population produces a hyper-reactive response to mold spores, but not James. Instead, James’s results suggested that he had more problems with actinomycetes bacteria and biotoxins.

While few mold studies have been done in ME/CFS, a large 2022 study, which unfortunately did not have a control group, found evidence of mold toxins in over 90% of ME/CFS patients who had a history of being exposed to a water-damaged building. A prior study reported a similar result – noting that an assessment of healthy controls by the same lab reported no positive results.

Treatment

Ritchie Shoemaker’s 12-step protocol

Dr. Heyman combined Ritchie Shoemaker’s 12-step protocol with his own integrative health approach. The full protocol is 12 steps but is stopped whenever a patient achieves health. Laboratory tests are given throughout the protocol to assess the patient’s state of health and provide treatment clues. A short outline is below. (See the 12-step protocol page for more.)

Create a safe living situation – The first step of the protocol involves removing the patient from a moldy house, school, or workplace.
Remove toxins using Welchol or cholestyramine.
Eliminate bacterial MARCoNS (Multiply Antibiotic Resistant Coagulase Negative Staphylococcus) from the nose, if present. A combination of therapies is used, including EDTA.
Gp on a gluten-free diet for three months if indicated by a positive antigliadin antibody (AGA) test.
Correct abnormal androgen levels using DHEA (dehydroepiandrosterone), HCG (human chorionic gonadotropin) injections (or sublingually) for 5 weeks, or VIP (vasoactive intestinal polypeptide) nasal spray for 30 days.
Correct antidiuretic hormone/osmolality problems with desmopressin tablets every other night for 10 nights or up to a month while watching osmolality closely.
Correct an inflammatory marker called MMP-9, an inflammatory marker with omega 3 fatty acids, usually EPA and DHA, in conjunction with a “No Amylose” diet (potatoes, sweet potatoes, peanuts, carrots, plus cereal grains).
Correct low VEGF 9 (<31) (vascular endothelial growth factor) if present, while staying on a no amylose diet.
Correct high levels of complement C3a using high-dose statins while adding CoQ10 10 days into the treatment.
Next, check for elevated C4a – while continuing with the rest of the protocol and VIP.
Reduce elevated TGFB1s – an innate immune factor – by treating with Losartan for 30 days in adults.
Add VIP if necessary – the website states that “By this time, most patients will already have become much better with reduction or resolution of at least 75% of their baseline symptoms.”. A normal blood test for lipase; a negative culture for MARCoNS; a normal HERTSMI-2; and a normal VCS test indicate that the patient’s toxin loads are low and VIP can be used if the patient is not back to health.

James’ Progress

Over the 16 months James has been on the protocol, he reported:”I’ve had slow but steady progress since I started the treatment protocol. At the time I was almost literally on my deathbed.”

I have also been treating gut health along the way (SIBO, etc.). Gut health is a huge component of this protocol and many mainstream doctors miss this. I noticed a significant change when we really targeted the gut around the 11-month mark or so with many treatments including biocidin, colostrum, calcium magnesium butyrate, pro bio spore/probiotics, collagen peptides, phosphatidylcholine (sunflower lecithins), digestive enzymes and SBI protect, which is gut immunoglobulins and BPC-157. The VIP I’m currently on also helps the gut.

I’m able to take foods like bananas and spinach and supplements like vitamin B12 and D3 that used to cause him problems.

A much healthier James – present day.

Currently, I’m on the last step which is focused on repairing brain inflammation and correcting the abnormal gene expression in one’s genome.

I can walk but am not able to exercise or drive; but I expect to continue my progress and eventually return to health. One year ago, I could not even fathom getting out of bed and using my laptop, or iPhone, cooking banana bread for my mom, or handling my finances. Now, this is all happening today as I continue on this path. Finally, I can say that my parents are much happier now and have less stress due to my progress and healing.

In summary, I do hope that this information for others is more than thought-provoking. I feel at times people feel validated or comfortable in their diagnosis. However, if you’re dealing with a chronic illness, and not getting any better with your current treatment, you need to really challenge things. I did and I’m winning.

One should be mindful and really ask yourself – am I on the right path? Is there possibly something else going on with my health and other avenues that I have not searched out? It’s easy to maintain a myopic view or even be conditioned by medical labels and diagnoses these days.

I have referred a close friend in the Boston area who was also initially diagnosed with ME/CFS, anxiety, and depression. He had a very similar experience as me, such as visiting numerous doctors and multiple trial medications, etc. Fortunately, I was able to refer him recently to Dr. Heyman and his GENIE test results showed CIRS stage 1. He just embarked upon his first six weeks of the treatment protocol. Stellar.

I also referred my father’s friend who was initially diagnosed with fibromyalgia and anxiety. She was put on anxiolytics, anti-depressants, and narcotics. Luckily, we placed her under Heyman’s wing and her recent GENIE test demonstrated CIRS stage 1 with severe neuronal injury.

There’s not a magical drug or supplement out there that will fix a chronic illness. It’s easy to treat symptoms all day long but unless the root cause is treated, the disease will remain. That’s why I believe it’s imperative to take a combination of functional and allopathic (conventional) medicine approaches. The root cause needs to be treated and the big picture needs to be evaluated. You just can’t treat the leaves on a tree…

My dad calls my illness a “Rip van Winkle type of syndrome”. I was critically sick and bedridden and unable to participate in or even keep up with my chosen profession (medicine) for so long that now that I’m coming back to life, I have a fresh perspective regarding where medical practice was and is. It’s been eye-opening, to say the least. I believe enough hard data and science exist to be able to confidently state that the CIRS paradigm of treatment has the potential to help many.

Each day for me is truly genuine recovery and a new light. My body is healing in a coordinated fashion as we have proceeded with each step of the protocol. My biomarkers and other lab values have demonstrated all of this and supported the research. My brain, cells, and mitochondria are actually healing. Talk about amazing science!!

I cannot thank Dr. Heyman enough for literally bringing me back to life, and also for Dr. Ritchie Shoemaker’s brilliance with the GENIE test and his dedication to biotoxin illness.

I’m a firm believer that everything on this journey happens for a reason. I’ve concluded there is definitely a Higher Source that still wants me on this earth to help others with chronic illness. I have not gone through all this pain and suffering for nothing, right?!

As my dad said to me on my birthday last week, new beginnings exist for me to help others. I couldn’t agree more.

Dr. Heyman has already discussed career coaching with me, and I will be shifting from an emergency medicine physician to a biotoxin/CIRS specialist. I am beyond thrilled and looking forward to becoming literate with the GENIE test and becoming certified after I complete the intense CIRS courses needed to treat patients. I will carry the utmost passion and empathy towards these patients I encounter, due to my journey through this chronic illness.

Lastly, I sincerely thank Cort Johnson for his interest in my story and passion for helping others. I appreciate him putting this information out there for people to absorb, research, and ultimately get themselves on the correct healing path if they feel this is applicable to them. I’m confident that it will only help!

Dr. James

If you’d like to communicate with James please provide your email address in the contact form for Health Rising and I will pass it on.
Find out more about Dr. Shoemaker’s approach including finding physicians using his techniques here
Dr. Heyman’s website
Support CIRS research here

Take the CIRS Poll!

Determine if your symptoms suggest – according to Dr. Shoemaker – you have CIRS. Also, if you’ve gone through the CIRS protocol, please tell us how it went.

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