A Beginner’s Guide to the CIRS Treatment Protocol
Why Am I Still Sick?– A Familiar Story
You’ve seen every specialist you can think of. Rheumatologists, neurologists, gastroenterologists in hopes of getting answers to your relentless fatigue, brain fog, pain, or mysterious skin and gut issues. The tests come back “normal.” Maybe you’re given a new diagnosis like fibromyalgia or chronic fatigue syndrome, but nothing really explains why your health collapsed after moving into that damp house or getting Lyme years ago.
If this sounds familiar, you may be dealing with Chronic Inflammatory Response Syndrome (CIRS). And while the road back to health can feel overwhelming, there is a structured, science-backed process that works: the Shoemaker Protocol.
In this article, we’ll walk you through Phase 1 of the CIRS treatment protocol—the first and most essential steps. It’s where every patient starts, and where the foundation for recovery is built.
What Is the Shoemaker Protocol?
The Shoemaker Protocol is the only peer-reviewed, evidence-based treatment plan for CIRS. Developed by Dr. Ritchie Shoemaker, it provides a stepwise approach to addressing the root causes of biotoxin illness. Instead of masking symptoms, the protocol systematically removes biotoxins, reduces inflammation, and restores normal immune and hormonal function.
The protocol is divided into eleven steps. Phase 1 is all about one thing: stopping further exposure to biotoxins. Phase one covers the first three steps of the shoemaker protocol:
- Removal from exposure
- Treating with binders
- Eradication of MARCoNS
Phase 1: The Foundation of Recovery
Step 1: Remove Yourself From Exposure
CIRS is triggered and sustained by ongoing contact with biotoxins (most commonly from water-damaged buildings, but also from Lyme, dinoflagellates, or other environmental sources). If you’re still exposed, nothing else you do will stick.
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This might mean testing your home with ERMI or HERTSMI-2 to identify hidden mold.
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It could involve workplace adjustments, temporary relocation, or remediation.
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Patients often struggle here, because exposure avoidance can mean big lifestyle changes. Step 1 is the single most important step of the entire protocol.
Without removing exposure, every other step of treatment is like bailing water from a sinking ship.
Step 2: Start Binders (Cholestyramine or Welchol)
Once exposure is controlled, the next step is to remove biotoxins already in circulation. That’s where binders come in.
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Cholestyramine (CSM): The gold standard binder. Prescription-only, it binds biotoxins in the gut and escorts them out of the body.
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Welchol (colesevelam): A gentler alternative for patients who can’t tolerate CSM.
How they work:
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Biotoxins are recirculated through bile in the digestive system.
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Without binders, they keep cycling endlessly.
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Binders interrupt this cycle, gradually lowering the biotoxin burden.
What to expect:
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Some patients feel worse at first (a “detox” effect as toxins mobilize).
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Over time, most notice clearer thinking, reduced fatigue, and improved stability.
Step 3: Address MARCoNS (if present)
MARCoNS (Multiple Antibiotic Resistant Coagulase Negative Staphylococci) are biofilm-forming bacteria that can colonize the sinuses in CIRS patients. They produce toxins that further suppress MSH (Melanocyte Stimulating Hormone), one of the hormones already low in CIRS.
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Testing is done via a nasal swab culture.
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If positive, treatment typically involves BEG spray (a compounded antibiotic/EDTA spray) or similar approaches to break down biofilm and eradicate infection.
Not every patient has MARCoNS, but for those who do, treating it early is essential.
Why Phase 1 Matters So Much
It might sound simple: remove exposure, start binders, treat MARCoNS if present but Phase 1 is where the real groundwork happens.
Here’s why it’s indispensable:
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Without it, later phases (like correcting hormones or immune signaling) won’t work.
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Patients who skip ahead often relapse.
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Even advanced interventions like VIP nasal spray fail unless the body is cleared of biotoxins first.
Think of it like building a house: if the foundation is cracked, it doesn’t matter how nice the roof is.
Common Challenges Patients Face in Phase 1
Identifying exposure
Mold testing can be confusing. Interpretation of environmental testing should be done by an experienced practitioner. There’s more to testing than having a HERTSMI score less than 10.
Remember, it’s not just mold that needs to be tested for. Additional environmental testing needs to be done for:
- Beta Glucans
- Endotoxins
- Actinomycetes
Even if you have a perfect HERTSMI, other biotoxins could be keeping you in exposure and therefore sick.
Binder intolerance
Cholestyramine can cause constipation, bloating, or GI upset. Proper dosing, hydration, electrolytes, and sometimes switching to Welchol helps.
Feeling worse before better
As toxins are mobilized, symptoms can flare temporarily. This doesn’t mean treatment is failing—rather, it means the process is working.
Navigating skepticism
Friends, family, and even other doctors may dismiss CIRS. Having objective labs (like TGF-β1, MSH, C4a, MMP-9, VEGF) helps validate the process.
What Improvement Looks Like in Phase 1
- Brain fog lifting—patients report they get glimpses of clear thinking.
- Energy stabilizing—it’s not that fatigue improves, but there’s a stabiliziation of energy. Fewer days where you’re completely bed bound.
- Fewer crashes—less post-exertional malaise, more resilience.
- Emotional relief—validation that symptoms are real, and a roadmap exists.
Phase 1 isn’t a quick fix, but it’s the turning point where patients shift from helplessness to empowerment.
Why Most Doctors Don’t Talk About This
Conventional medicine isn’t trained in biotoxin illness. Cholestyramine, for example, is usually prescribed for high cholesterol—not mold toxicity. Most physicians never learn that MARCoNS exists, let alone its role in CIRS. That’s why patients so often feel lost until they connect with a CIRS-literate provider.
At Flourish Clinic, we emphasize Phase 1 education because when patients understand why these steps matter, adherence and outcomes improve dramatically.
Know this
Phase 1 of the CIRS treatment protocol is about clearing the battlefield. By removing ongoing exposure, using binders to lower the toxic load, and treating MARCoNS if present, you give your body the best possible chance to heal.
Every step after this builds on the foundation laid here. Skipping ahead almost always backfires. But if you commit to Phase 1, you’ve already started the journey out of chronic illness.
FAQ: Phase 1 of CIRS Treatment
Q: How long does Phase 1 last?
It depends. Some patients stabilize in a few months, others take longer. It’s based on how quickly exposures are controlled and how well binders are tolerated.
Q: What if I can’t tolerate cholestyramine?
Welchol can be used as an alternative. Dose adjustments, slower titration, and gut support can also improve tolerance.
Q: Do I have to move out of my house?
Not always. Some homes can be successfully remediated. But if testing shows very high mold scores, relocation be be necessary.
Q: Can I skip straight to medications like VIP spray?
No. VIP only works after inflammation is controlled and biotoxins are cleared. Skipping steps leads to relapse.
