Why Treating Chronic Infections Too Early Often Fails in CIRS
Introduction: When Treatment Timing Becomes the Limiting Factor
As recovery from CIRS progresses, attention often turns to chronic infections. Lyme, Bartonella, parasites, gut infections, and other microbial burdens are frequently suspected, and often correctly so. What follows is often a predictable sequence: antimicrobial treatments are initiated, symptom burden increases, tolerance diminishes, and progress stalls.
This pattern raises an important question: if infections are part of the problem, why does treatment so often fail to produce sustained improvement?
The answer is not that infections are irrelevant, nor that treatment is misguided. Rather, the issue is timing. In CIRS, the immune system often lacks the capacity to properly recognize, prioritize, and respond to internal threats. Until that capacity is restored, even well-chosen treatments can backfire.
This article introduces a framework for understanding why chronic infection treatment so often fails early in CIRS, and why immune readiness must come first.
Acute vs. Chronic Infections: An Important Distinction
Not all infections behave the same way in CIRS. Acute infections, such as a recent tick bite followed by early symptoms, are often easier for the immune system to detect and address, even in the context of biotoxin illness. In these cases, testing may be positive early, and treatment can lead to clear improvement.
Chronic infections are different. They unfold over years or decades, often quietly, and frequently coexist with long-standing environmental exposure. In these situations, the immune system has adapted, not by resolving the threat, but by misdirecting its attention.
Many CIRS patients fall into this chronic category. Their immune systems are not failing due to lack of effort, but due to misallocation of resources.
Immune “Attention” in CIRS: A Useful Analogy
One helpful way to understand this phenomenon is to think of the immune system as having a limited attention span.
In CIRS, exposure to biotoxins from water-damaged buildings, actinobacteria, endotoxins, and other environmental signals keeps the innate immune system in a constant state of high alert. These external threats dominate immune attention, leaving less capacity to detect and manage internal infections.
This creates a state of misallocated immune attention:
The system reacts intensely, but inefficiently
It struggles to prioritize threats
It responds broadly instead of precisely
In this state, chronic infections may be present, but they are not being properly engaged. Instead, attempts to treat them can amplify inflammation without leading to resolution.
The Role of MSH and Immune Coordination
A central feature of CIRS is the loss of melanocyte-stimulating hormone (MSH). This loss has widespread consequences, including impaired immune coordination, increased tissue permeability, and dysregulated inflammatory signaling.
Low MSH affects the integrity of mucosal barriers such as the sinuses, skin, and gut. These tissues become more permeable and more vulnerable to colonization. Over time, this can allow secondary microbial burdens, such as MARCoNS or actinobacteria, to take hold, further compounding immune confusion.
Importantly, MSH loss does not simply weaken the immune system; it disorganizes it. Without proper signaling, immune surveillance becomes erratic, and the ability to distinguish between meaningful threats and background noise is reduced.
Why Testing Is Often Negative or Inconclusive
This immune misdirection helps explain a common frustration among CIRS patients: negative or equivocal chronic infection testing (e.g., Lyme, Bartonella) despite strong clinical suspicion.
When immune attention is dominated by environmental threats, antibody production and cellular immune responses to chronic infections may be blunted or inconsistent. Tests that rely on these signals may fail to capture what is happening beneath the surface.
In many cases, testing only becomes positive after immune coordination improves. This is not because the infection suddenly appeared, but because the immune system has regained the capacity to recognize it.
Why Antimicrobials Can Make Things Worse
When antimicrobial treatments are introduced before immune readiness is restored, several outcomes are common:
Symptoms flare without resolution
Tolerance rapidly declines, even at low doses
Patients feel “toxic” or destabilized
Progress plateaus or reverses
This is not a sign that treatment is too weak. Often, it is a sign that treatment is happening too early.
Without adequate immune coordination, antimicrobial interventions can increase inflammatory signaling without effectively clearing the target. The result is more immune noise, not better immune focus.
The First Three Steps as Immune Gatekeepers
In CIRS treatment, the initial phases of treatment are often viewed as preparatory. Their deeper role, however, is to restore immune attention.
These steps include:
Reducing ongoing environmental biotoxin exposure
Lowering circulating biotoxin burden with Cholestyramine or Welchol
Addressing microbial colonization in the sinuses that perpetuates immune activation
Together, these interventions quiet the loudest external signals and reduce background inflammation. This allows the immune system to gradually shift its focus inward, especially once MSH production is restored.
Importantly, this process is not about achieving perfection. No environment is free of microbes or toxins. The goal is simply to lower the dominant signals enough for immune recalibration to occur.
What Immune Readiness Looks Like
Immune readiness does not mean full recovery. It shows up subtly, through trends rather than endpoints.
Examples include:
Gradual increases in MSH from very low levels
Improved performance on visual contrast sensitivity testing
Partial normalization or directional movement in inflammatory markers
Reduced symptom volatility
Improved tolerance to binders or supportive therapies
These changes suggest that immune attention is becoming more organized—even if many markers remain abnormal.
At this stage, the immune system is no longer fully consumed by environmental threat detection. Space opens up for addressing internal burdens.
Why “Doing More” Is Not Necessarily the Answer
When patients feel stuck, the instinct is often to escalate: stronger antimicrobials, more supplements, more aggressive protocols. In CIRS, this approach can backfire.
The issue is not insufficient intensity, but incorrect sequencing. Until immune attention is restored, increasing pressure on the system tends to amplify dysfunction rather than resolve it.
Setting the Stage for the Next Phase
Once immune readiness begins to emerge, patterns often become clearer. Symptoms that once blurred together start to separate. Lab markers fluctuate in more interpretable ways. Infection categories that were previously hidden begin to reveal themselves.
This is where thoughtful assessment of chronic infections becomes not only possible, but productive.
The next step is learning how to recognize those patterns, and how to understand which infection pathways may be most relevant once immune attention has shifted.
