Tick-Borne Illness, Chronic Lyme Disease and CIRS: Why Regulating Inflammation Comes First

At The Autoimmune Clinic, we often support individuals navigating the complex aftermath of tick-borne infections. These cases are rarely straightforward. While Lyme disease (Borrelia burgdorferi) is the most well-known, ticks can transmit a wide array of pathogens—including Babesia, Bartonella, Anaplasma, Ehrlichia, and Rickettsia. Moreover, not all of these infections are exclusive to ticks. For example, Bartonella may also be acquired through animal scratches or flea bites, while Babesia and Rickettsia have been identified in certain regions as potentially mosquito-transmissible.

This broader range of vectors means that exposure may occur without clear recollection of a tick bite—particularly in individuals with outdoor occupations, frequent pet contact, or international travel histories. Often, multiple infections (co-infections) are present, further complicating diagnosis and treatment. It is no wonder that many people go years without adequate answers or relief.

Yet, an equally important truth is often overlooked: the immune system, not simply the pathogens themselves, plays a central role in driving ongoing symptoms.

The Challenge of “Chronic Lyme” and Persistent Symptoms, is it CIRS?

The term "chronic Lyme disease" remains controversial in conventional medicine. Nevertheless, a growing number of patients report long-term, multi-system symptoms following acute infection—fatigue, brain fog, joint or nerve pain, and dysautonomia among the most common. In such cases, antimicrobial treatment alone frequently fails to produce lasting relief.

Why? Because what is labelled as “chronic infection” may in fact be an entrenched state of immune dysregulation and systemic inflammation, not ongoing microbial replication. This is especially relevant in individuals with a genetic predisposition—particularly certain HLA-DR haplotypes—which impairs their ability to clear biotoxins effectively and renders them more susceptible to developing Chronic Inflammatory Response Syndrome (CIRS).

When the Immune System Becomes the Driver of Disease

In CIRS, the immune system remains in a chronically activated state long after the initial pathogen may have been cleared. Instead of resolving, the immune response becomes dysregulated—producing inflammatory mediators, impairing detoxification, and perpetuating neuroimmune and endocrine dysfunction.

Attempting to treat persistent symptoms with aggressive antimicrobial protocols—without first regulating immune function—can further destabilise an already overwhelmed system. This can result in worsening inflammation, heightened sensitivity to treatment, or even the onset of new symptoms. In our clinical experience, this is one of the most common patterns seen in clients who have seen multiple specialists or undergone repeated courses of antibiotics or herbs, with minimal improvement.

Why Immune Regulation Must Come First

Stabilising the immune system is the essential foundation before initiating targeted antimicrobial therapies. This approach reduces reactivity, improves tolerance, and enhances the body’s capacity to respond to treatment more effectively and sustainably.

A stabilising phase may include:

• Identification and removal of ongoing exposures, such as mould in the home or workplace, which perpetuate biotoxin load and immune activation.

• Use of binders to support the clearance of inflammatory toxins (including mould toxins, bacterial by-products, and neurotoxins).

• Correction of nutrient deficiencies and mitochondrial dysfunction, which often underlie fatigue and cognitive issues.

• Nervous system regulation and limbic system support, which are vital for downregulating neuroinflammation and restoring parasympathetic tone.

• Support for detoxification pathways, including bile flow, antioxidant status, and cellular repair mechanisms.

Only once this groundwork has been laid can we begin to accurately assess the true burden of pathogens and explore selective, well-tolerated antimicrobial support—if still clinically warranted.

A Functional Medicine Approach to Chronic Tick-Borne Illness

Our approach at The Autoimmune Clinic is rooted in the principles of systems biology and patient individuality. Rather than pursuing pathogens at all costs, we consider the terrain of the host: genetic predisposition, environmental triggers, immune regulation, detox capacity, and resilience.

By placing immune system regulation at the centre of our strategy, we aim not only to reduce symptoms, but to support long-term healing and resilience. For many, this approach is the turning point after years of chasing microbes without meaningful or lasting relief.

If you're navigating persistent symptoms following a tick-borne illness or suspect you may be dealing with immune dysregulation or CIRS, our team is here to support you with evidence-informed, individualised care.

Muriel Wallace-Scott, our Clinic Director, is a Certified Shoemaker Proficiency Partner and has completed advanced training under Dr Ritchie Shoemaker’s CIRS protocol.

This ensures that clients at The Autoimmune Clinic receive care grounded in the most up-to-date, validated approach to biotoxin-related illness.

If you suspect that CIRS could be the missing piece in your health journey, you're welcome to book a 30-minute discovery call with Muriel to explore whether this framework might apply to your case—and what the next steps might look like.

Book a Discovery Call