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I worked with Dr Shoemaker to create a thorough yet easily absorbed "101" guide summarizing his work on mold illness (aka CIRS).


Dr. Shoemaker's Mold/CIRS (Chronic Inflammatory Response Syndrome) 101 for Patients !


The information on Mold illness (Dr Shoemaker calls it CIRS - Chronic Inflammatory Response Syndrome) can be overwhelming. Here is condensed information to make your life easier! (This information was gathered by a patient. Please follow your doctor’s advice.)

Nifty new things:
CIRS (Chronic Inflammatory Response Syndrome aka Mold Illness) 101 Course Outline
  • CIRS, Dr Shoemaker, The Shoemaker Protocol
  • Finding a Safe Living/Work space, Testing/Inspecting/Remediating/Cleaning
  • Medications, Lab Tests
  • Diet, Supplements, Lifestyle
  • Resources
Part One: CIRS, Dr Shoemaker

“Mold Illness”
  • Generic term for illness due to inflammation caused by inhaling toxins in a water damaged building.
  • Some people can’t remove biotoxins as well as others, due to their genetics. The antigens stay in the body, and our own defenses bombard our body in response to those antigens.
  • A general term is “biotoxins” - fungi, bacteria, mold, spores from molds, VOCs, etc. They can all cause inflammation via inhalation.
  • The inflammation mold causes can affect every system of the body - hormones, brain function...causing a long list of symptoms like: fatigue, pain, cognitive/psychiatric issues, sleep disturbance, etc.
  • Mold Illness can be diagnosed as chronic fatigue, depression, fibromyalgia, MS, lupus, Lyme disease, inflammatory bowel disease, irritable bowel, etc. Many conditions have symptom overlap.
The Biotoxin Pathway

The Biotoxin Pathway (large clear version) diagram sums up CIRS nicely.

Screenshot 2017-03-30 at 1.24.39 PM.png

Papers with in-depth information:
HLA-DR and HLA-DQ Immune System Genes
  • Control your immune system’s antigen response to biotoxin exposures.
  • About 25% of the population is more genetically susceptible. Within the 25% there are variations. People with certain HLA combinations (haplotypes) won't be able to create effective antibodies to biotoxins from mold and bacteria from WDB, Lyme, dinoflagellates/ciguatera or any of those if multisusceptible.
  • There are other genes involved as well, research is being done in this area and more advanced diagnostics will be available. The inflammation in CIRS causes hundreds of other genes to become dysregulated in their expression (turned off or on). Dr Shoemaker has developed a genomic test which shows the expression of these genes called Progene DX. This will be a useful tool in diagnosis and treatment of CIRS especially in complex cases as it will show specific fingerprints for mold, Lyme, ciguatera and MARCoNS.
Dr. Ritchie Shoemaker, MD
Shoemaker Protocol

The protocol fixes problems step by step. Not every patient is the same, so you need a certified doctor to guide you. 14 Step Plan Explained. You start at the bottom of the pyramid and go to the top.

The very difficult first step is limiting further exposure to water damaged buildings. Requires lifestyle changes.
  1. Test your home/office with Mycometrics ERMI/HERTSMI DNA testing.
  2. Hire a mold inspector. Greg Weatherman - in person and FaceTime/Skype consulting/referrals/advice (wrote chapter in Shoemaker’s book). Michael Schrantz (Tucson, Arizona)
  3. Fix issues (remediate), or possibly move.
  4. If you feel bad somewhere, follow your instincts!
  5. More on this in Part Two.
Get a Baseline (retest regularly)
  1. “VCS” vision test online (cheap) or at doctor’s office. (Note: some patients pass the test despite having CIRS)
  2. Shoemaker blood labs (varies by patient). Most available at Quest Diagnostics, some only Labcorp (HLA DR by PCR, MSH, MMP9).
    1. HLA calculator (figure out your results). Also see "Rosetta Stone" in the books Mold Warriors or Surviving Mold and the HLA chart on this page. Visit a knowledgeable provider to confirm your reading.
    2. Fill in your HLA genes, share with others:
    3. Physician’s Lab Sheet with all Shoemaker labs and specific codes
  3. Nasal swab test for MARCoNs (at doctor’s or kits mailed free to your home - Microbiology Dx). Note: People are also doing a dental scan called “3d cone beam ct scan” related to MARCoNS problems.
  4. Neuroquant Brain MRI (if possible). Has volumes of 11 brain regions, can help determine if damage is from mold vs Lyme, etc. Detects things a standard MRI cannot.
    1. Neuroquant Introductory Video with Shoemaker
    2. Cortechs Labs, creator of Neuroquant technology
      1. Find a Neuroquant compatible MRI center
      2. Example of “General Morphometry Report” - volumes of 11 brain regions, left and right side.
Find a Shoemaker-Certified Doctor

Do your standard blood tests look normal but you feel bad? Have you been told “it's all in your head”? Find a doctor who understand
Top Three Things

If you have been diagnosed with CIRS by a Shoemaker certified doctor, the top things you can do are:
  • Avoid poor quality (indoor) air.
  • Stick with treatment - there is HOPE!
  • Get support.
Part Two: Safe Living/Work Space, Testing/Inspecting/Remediating/Cleaning

Safe Living/Work Space

Limiting your exposure while treating CIRS allows you to heal faster. This is hard, there are many water damaged buildings (up to 50%). It is essential.

Testing methods - ERMI/HERTSMI

These are EPA validated DNA-based tests. You can fill out a form on to get sampling supplies mailed to you. Or you can use your own clean dry Swiffer cloth and print this PDF form.

See the HERTSMI-2 paper Shoemaker, R.C. & Lark, D. (2016). HERTSMI-2 and ERMI: Correlating Human Health Risk with Mold Specific qPCR Water-Damaged Buildings, IEP Appendix B (p26), Indoor Environmental Professionals Panel of Surviving Mold Statement.

Run a HERTSMI test (~$150) on your home/work using Mycometrics Mycology Lab. An ERMI test (~$350) can tell you even more information.

  • Testing the whole house versus single room versus single floor...
  • Existing dust versus sampling from plastic bags/bins left out for a certain period…
  • Swiffer cloth versus vacuum method...
  • Testing indoors, or also outdoors as a “control”...
  • **Ask your doctor what’s best for your situation and how to perform the tests**
Note: ERMI/HERTSMI tests are not perfect, but are a very helpful diagnostic tool. They give you an idea of your air quality. Mycometrics, your doctor, and other experts can explain your test results.

Home Inspection

A visual inspection can find things no test can. In general, mold inspections will involve the use of special equipment like moisture sensors, cameras, etc. **Make sure to check your entire home (crawlspace, attic, etc)**

Finding an inspector who understands CIRS can be hard. Greg Weatherman is Shoemaker-backed and offers in-person (East Coast) and FaceTime/Skype consultations and can help oversee inspection/remediation and suggest local inspectors. He can also explain ERMI/HERTSMI test results.

Michael Schrantz in Tucson, Arizona. Also travels.


Remediation is the fixing of water damaged portions of a building. It can be expensive, time consuming, and expose you and your belongings to contamination. Seek out an expert like Greg Weatherman to assist you.


To keep your space clean, some simple ideas are:
  • Use “true” HEPA filters, move them around your rooms. Perhaps start with a less expensive model like Honeywell. Models with charcoal are good for odor reduction. Higher end models are made by IQ Air and Austin Air but if you need to move and replace filters it can be expensive. Note: A small HEPA filter cannot “fix” major indoor quality issues like a bad HVAC system, moldy basement, etc.
  • Dr Shoemaker praises Air Oasis air cleaners. They use different technology than HEPA and deal with the ultra fine particles HEPA can miss.
  • “Quat” (Windex/Fantastic etc) clean items.
  • Use vacuums with HEPA filters. Inexpensive: Shark. Expensive: Miele
  • Dry Swiffer cloth rooms.
  • Wash bedding/clothing regularly, Borax can be used in addition to standard detergent.
  • Consider “cross contamination”, if you bring items from an unsafe place into your space. Think: Bringing items from a musty place into your house. Moving old books/papers.
Part Three: Medications, Lab Tests


Closely follow your doctor's orders!

Cholestyramine (CSM) and Welchol are “binders” that you take orally to remove biotoxins. See the CSM Fact Sheet. This is a large topic, the information below only scratches the surface.
  • They remove biotoxins (you poop them out). Start with a low dose!
  • CSM is more powerful and is taken away from food, Welchol is usually taken with food. Take away from supplements and other medications. Ask your doctor about timing.
  • There are a few types of CSM: “Standard” packets/tub which insurance usually covers but has additives, “Pure” compounded, “Light” (avoid).
  • Most use the standard form. CSM can be constipating, helpful: extra magnesium, fruit, vitamin c, fiber.
  • Other binders like charcoal/clay/zeolite have not been published by anyone as effective.
BEG spray is sprayed up the nose to get rid of a MARCoNS infection in the sinuses (antibiotic resistant staph infection, common in CIRS patients).

VIP spray is sprayed up the nose. It can offer the CIRS patient many benefits and is typically used at the end of the protocol. Dr Shoemaker has shown in studies that it can sometimes help reverse brain damage.

*** BEG, VIP, CSM Suppliers List 5/16 *** - contact info, shipping costs, additional info.

Losartan is a blood pressure medicine sometimes used in the protocol to help lower the inflammation marker called TGFb1.

Desmopressin for fluid balance, etc. Must only be used by providers confirmed to know safety protocols.

Other medicines sometimes used are DHEA/HCG for hormones. *For men, using testosterone injections or cream isn’t advised*. Clomid is another option.

Lab Tests

Shoemaker blood labs are performed mostly at Quest Diagnostics, but some are only available at Labcorp (HLA DR by PCR, MSH, MMP9).

Some of the special tests can be tricky for the labs to run (ask them to carefully process them) and it may take some time for results to come back. C4a can take a month.

Study the Physician’s Lab Sheet with specific codes for the two labs. There are many potential tests to run. If you can, running most of them initially can be helpful. Only running a few might skip something important. Ask your doctor.

Part Four: Diet, Supplements, Support


In general, fresh (organic if possible), whole food is best. It is expensive to eat this way and not everyone can afford it, so just try your best! This is a huge topic. For some, food allergy testing can help determine sensitivities, and a nutritionist can be helpful, etc.


There are so many supplements available, follow your doctor’s advice!

A multivitamin is probably useful for most. Dr Shoemaker often recommends high dose fish oil (2.4 grams EPA, 1.8 grams DHA), especially during certain phases of the protocol. Check fat soluble vitamins A,D,K,E especially when on CSM long term.


CIRS can be a very difficult and isolating disease. Seek out help!
Other simple ideas to support yourself:
  • Take frequent showers, especially if you’ve gone out. Change clothes.
  • Try to keep moving, but don’t overdo it. Pushing too hard with aerobic activities can set you back. Think: stretching, light yoga, short walks.
  • Use an alarm on phone for reminders for taking meds etc.
  • Spend time outdoors.
  • Connect with others.
Part Five: Resources

Home testing
Nasal culture testing
Indoor Air Quality Experts
Brain Imaging
Facebook Groups
Hepa Filters/Air Cleaners
Respirators/Face masks
  • Mold Illness Made Simple - An eight week online course that allows you to grasp the key concepts and science of CIRS, at your own pace.
  • Like
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chris graber
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Excellent! Thanks. As a mold survivor myself - this would have been a great resource. Would have been helpful to have it all in one place, rather than fumbling through what to do. Mold gives severe disability and brain fog. When in that disabled state, we need someone to talk us through and guide us. It's nearly imposible to do on your own at that level of unwellness.

Whoa - what a great resource. I will use it in the blogs...Thanks!
Excellent. thank you.
Fantastic. Biotoxin illness in bullet form
Great primer for those wanting to get started with the Shoemaker protocol!

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