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About CIRS and the Shoemaker Protocol


Chronic inflammatory conditions come in different shapes and sizes. They can have different exogenous triggers that are in turn mediated by endogenous characteristics, such as deficiencies/excesses, whether we are glycotoxic, our microbiome, how good our vascular health might be, auto-immunity and of course genetics.

Chronic Inflammatory Response Syndrome (CIRS) was first used by Dr Shoemaker as a term in the 1990s to describe a multi-symptom, multi-system chronic illness. Exposure to certain environmental ‘inflammagens’ and pathogenic organisms (which can collectively be termed ‘biotoxins’) is understood to trigger this chronic inflammatory response in the body.

Having identified CIRS, Dr Shoemaker then created a Protocol to work patients through a recovery process.  The 12 step Shoemaker Protocol has now been in place for over 25 years and as his latest 2025 paper shows, has been instrumental in supporting thousands of people around the world understand their symptoms and recover their health.

Dr Shoemaker


The Science Behind the Shoemaker Protocol

CIRS is a term first applied to the response to exposure to Pfiesteria in the Pocomoke river. It now specifies the following environmental exposures as being key considerations for triggering a chronic inflammatory response:

  • Post Lyme syndrome (CIRS-PLS), which occurs beyond the acute phase of Lyme disease in around 20% of Lyme patients.
  • Ciguatera poisoning (CIRS-Ciguatera) is a fish borne dinoflagellate that can trigger neurologic and gastrointestinal symptoms when consumed. Around 5% of cases are thought to become chronic.
  • Cyanobacteria (CIRS-Cyanobacteria) is a blue-green algae that can produce toxic substances, and that can have hepato and neuro-toxic effects.
  • A bite from a brown recluse spider is also known to be a trigger of the same chronic immune response.

Whilst mould and exposure to water-damaged buildings (CIRS-WDB) are probably the most well-known in Europe, it is important to understand that the toxic soup found in a water damaged building may not be the only trigger.

In 2008, the US Government Accountability Office (GAO) delivered a case definition with four criteria for a CIRS diagnosis. Firstly, demonstration of exposure to water damaged building(s). Secondly, signs and symptoms consistent with exposure. Thirdly, laboratory testing consistent with results seen in published studies and lastly, improvement with appropriate therapy. The Protocol is split out into 12 steps. The first being remove from exposure.

To check an environment for key moulds, the most common tests that can be easily undertaken by self-testing of an environment are the Environmental Relative Moldiness Index (ERMI) and Health Effects Roster of Type Specific Formers of Mycotoxins and Inflammagens (HERTSMI 2), utilising dust sample collection. Eradicating MARCoNs comes next and re-balancing all other out of normal range markers from laboratory testing follows until all re-tests are normal. Colab Services Ltd. offer all these tests.

With volumetric MRI testing and NeuroQuant reporting we can now see changes consistent with exposure to CIRS-PLS and CIRS-WDB reflected in the brain. Different parts of the brain can show oedema or atrophy consistent with lab work. Improvements can also therefore be tracked with repeat scans. The work that Dr Shoemaker has published on brain changes ties in with the work of Dale Bredesen on cognitive decline, such that he has defined CIRS as being part of the pathology of type 3 Alzheimer’s.

Both Doctors also agree that resulting inflammation and eventual hypo-metabolism are the net result of inflammatory exposures, contributing to changes in brain function. CIRS can, therefore, be seen as very much part of the cognitive decline jigsaw. Once CIRS has been identified, the Shoemaker protocol can be undertaken in a pyramid fashion. Starting from the bottom, the steps are followed until the top is reached. The first step and most important is the removal of exposure to the biotoxin. Whether the exposure is school, home, work, a frequently visited service or gym, it is important to prevent exposure to inhaled contaminants. If this is not achieved, the inflammatory cycle may not be arrested.

CIRS Started with an illness in fisherman in the Pokomoke area of Maryland, by chance the area that Dr Shoemaker was a practising family physician. He has dedicated his life to this syndrome, and mapped it out in 2011 via the Biotoxin Pathway diagram.

Download the diagram

The future of CIRS is expanding into transcriptomics with new tests such as the genomic expression by Nanostring: inflammation explained (GENIE) revealing signature changes in gene expression, protein production and cellular activity, leading Dr Shoemaker to note that “if you don’t know the transcriptomics, you don’t know the illness”.

Download the brochure

Training in CIRS and the Shoemaker Protocol

For practitioners wishing to find out more about becoming a Proficiency Partner of CIRSX please contact [email protected]

Colab Services Ltd cover all aspects of the CIRS:

  • We host an annual Foundation Training course in CIRS, called the Biotoxins in Clinical Practice Course (Training delivered by CIRS Academy)
  • Relevant blood tests that are from laboratories used in CIRS related studies so the results can be contextualised with correct laboratory reference values.
  • Technical support for laboratory results.
  • Support with accessing MRI volumetric brain scans.
  • Direct access to the GENIE transcriptomics test.

Testing via Colab Services

Full testing for CIRS and the Shoemaker Protocol is available via Colab Services Ltd.

Our test selection includes:

Our Test
Q97 Practitioner designed CIRS Panel 1
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Q98 Practitioner designed CIRS Panel 2
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Q99 Practitioner designed CIRS Panel 3
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Q100 CIRS Elite (2017 diagnostic panel)
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Q150 CIRS Lite
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Q160 CIRS Comprehensive
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Q170 CIRS Express Panel
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Q190 CIRS Ultimate (includes HLA cheek swab)
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KA910 HLA Cheek Swab
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Q97112 HLA blood test
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PD501 GENIE test
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EM205- ERMI/HERTSMI testing (plus the whole dust swiffer range)
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NQ551 NeuroQuant
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View All Our Immune System/Defence tests

Latest

Dr Shoemaker continues to research and publish on CIRS. His latest paper has just been published in the European Society of Medicine, Medical Research Archives, Volume 13, Issue 8 in which he reviews 30 years of published research on human health effects of exposure the interior environment of water-damaged built environments.

Download Me
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Scientific Updates

Latest Papers 


Related Colab Education Videos on the CIRS / Shoemaker Protocol

Do speak with a member of the Colab Services Team if you wish to learn more or be notified of upcoming events related to this topic.