Are Chronic Infections the Hidden Root Cause of Multiple Sclerosis?

A Functional Medicine Approach to Uncovering Triggers and Supporting Recovery
By Dr. Lisa Ballehr

Understanding MS as a Multifactorial Condition

Understanding the complex nature of chronic infections as the hidden root cause of Multiple Sclerosis is a key step in shifting from symptom management to root-cause healing. Multiple Sclerosis is a neurodegenerative and autoimmune condition with a wide range of contributing factors, including chronic infections, environmental toxins, mitochondrial dysfunction, and gut-immune imbalances. Rather than suppressing symptoms with conventional therapies alone, a functional medicine approach seeks to identify and address these underlying causes.

Chronic Infections: A Major Trigger for Autoimmunity

Emerging research and clinical evidence suggest that chronic infections may be the hidden root cause of Multiple Sclerosis in many individuals. These infections can trigger immune dysregulation through molecular mimicry, prolonged inflammation, and disruption of the gut-brain-immune axis.

1. Epstein-Barr Virus (EBV)

One of the strongest infection-related triggers, Epstein-Barr Virus has been closely linked to the development of Multiple Sclerosis. Studies show that EBV proteins resemble myelin, prompting the immune system to mistakenly attack the nervous system.

Testing: EBV early antigen, nuclear antigen, and PCR for chronic viral activity.
Treatment: Antiviral herbs such as monolaurin, olive leaf, and lysine, along with immune-balancing strategies.

2. Human Herpesviruses (HHV-6, HHV-7, CMV)

These viruses are often detected in lesions of patients with Multiple Sclerosis and may contribute to ongoing neuroinflammation. HHV-6, in particular, can reactivate during stress or immunosuppression.

Treatment: Valacyclovir or herbal antivirals, in addition to Low-Dose Naltrexone (LDN) for immune modulation.

3. Tickborne Infections (Lyme and Co-Infections)

Pathogens such as Borrelia burgdorferi (Lyme), Bartonella, and Babesia can mimic Multiple Sclerosis symptoms, making diagnosis and treatment challenging. These infections can directly affect the nervous system and impair mitochondrial health.

Testing: IGeneX, Vibrant Tickborne Panel, and CD57 NK cell test.
Treatment: Herbal or antibiotic antimicrobial protocols, alongside immune and detox support.

4. Mycoplasma Pneumoniae

This stealth infection may persist intracellularly and is known to trigger autoimmunity. Mycoplasma pneumoniae could be an overlooked contributor to the hidden root cause of Multiple Sclerosis in some patients.

Treatment: Doxycycline, azithromycin, and immune-supportive agents like N-acetyl cysteine (NAC).

5. Chlamydia Pneumoniae

Capable of breaching the blood-brain barrier, this bacterium is another potential infection that may trigger or exacerbate Multiple Sclerosis symptoms.

Treatment: A combination of antibiotics or herbal antimicrobials and gut-immune support.

6. Candida and Fungal Overgrowth

Fungal dysbiosis contributes to gut permeability, systemic inflammation, and immune dysregulation. This may serve as a co-factor in those with Multiple Sclerosis linked to chronic infections.

Testing: Organic Acids Test (OAT) and GI-MAP stool analysis.
Treatment: Caprylic acid, oregano oil, berberine, and antifungal medications if needed.

7. Chronic Mold and Mycotoxins

Exposure to indoor molds and their mycotoxins can damage both immune and neurological function. This toxic burden may underlie chronic inflammation in some Multiple Sclerosis cases.

Testing: Mycotoxin urine testing (Great Plains or RealTime Labs).
Treatment: Mold remediation, detox binders (activated charcoal, chlorella), and liver support.

The Functional Medicine Approach: Personalized, Root-Cause Care

In functional medicine, treatment goes far beyond simply managing symptoms. The goal is to reverse dysfunction by restoring balance to the immune system, gut microbiome, mitochondria, and detox pathways. For those with Multiple Sclerosis potentially driven by chronic infections, a multi-layered, personalized plan is essential.

1. Reduce Inflammation and Immune Dysregulation

• Identify and eliminate triggers such as gluten, dairy, processed foods, and food sensitivities.
  
• Correct the omega-3 to omega-6 fatty acid ratio to calm inflammation.
  
• Treat infections like EBV, Lyme, Candida, and Mycoplasma, which may represent chronic infections at the hidden root of Multiple Sclerosis.
  

Key supplements:

• Vitamin D3 + K2 (5,000–10,000 IU/day)
  
• Curcumin, resveratrol, and quercetin
  
• Medicinal mushrooms (Reishi, Lion’s Mane)
  
• LDN for immune regulation
  

2. Restore Gut Health and Microbiome

Leaky gut and dysbiosis are common in autoimmune conditions. Functional gut healing is foundational in addressing chronic infections—the hidden root cause of Multiple Sclerosis.

The 4R Gut Protocol:

• Remove: Inflammatory foods, toxins, and infections
  
• Replace: Stomach acid, digestive enzymes, bile support
  
• Repopulate: Probiotics (50+ billion CFUs), fermented foods
  
• Repair: L-glutamine, aloe, DGL, and colostrum or IgG therapy
  

Testing for zonulin can assess gut permeability, and interventions like bone broth fasting can accelerate gut healing.

3. Support Mitochondrial Health

Mitochondrial dysfunction is central to Multiple Sclerosis progression. Restoring energy metabolism can slow neurodegeneration and promote nerve repair.

Key nutrients:

• CoQ10 (200–400 mg/day)
  
• PQQ, L-carnitine, alpha-lipoic acid
  
• NAD+ precursors (NMN or NR)
  

Lifestyle practices:

• Intermittent fasting or ketogenic diet to fuel neurons with ketones
  
• MCT oil and exogenous ketones for energy stability
  

4. Detoxification and Toxin Clearance

Many people with Multiple Sclerosis linked to chronic infections also carry a high toxic burden—heavy metals, pesticides, plastics, and mold toxins.

Detox strategies:

• Infrared sauna
  
• Binders: activated charcoal, modified citrus pectin, bentonite clay
  
• Liver support: glutathione, NAC, milk thistle
  

Heavy metal testing is recommended (urine or hair analysis), with chelation therapy under professional guidance if necessary.

5. Hormonal Balance and Stress Reduction

Stress and hormonal imbalances can worsen immune dysfunction. Functional medicine supports adrenal health and the HPA axis in individuals with Multiple Sclerosis driven by chronic infections.

Key strategies:

• Cortisol testing (DUTCH or saliva)
  
• Adaptogens: ashwagandha, Rhodiola, licorice root
  
• Magnesium, vagus nerve stimulation, and trauma healing therapies (EMDR, somatic work)
  

6. Lifestyle and Nervous System Support

A comprehensive lifestyle plan is essential for long-term healing.

• Exercise: Gentle movement (yoga, resistance training, rebounding)
  
• Sleep: 7–9 hours of deep rest, supported by magnesium, GABA, melatonin
  
• Emotional healing: Breathwork, cold exposure, acupuncture, and somatic therapy all support vagus nerve activation and reduce inflammation.
  

7. Advanced and Adjunctive Therapies

For some, advanced therapies may be required in conjunction with addressing chronic infections—the hidden root cause of Multiple Sclerosis.

• LDN (1.5–4.5 mg/day) for immune regulation
  
• IV therapy: Glutathione, NAD+, Myers’ cocktail
  
• Stem cell therapy (emerging area of research)
  

Summary: A New Paradigm for Healing

To effectively support those with Multiple Sclerosis, we must shift our paradigm from suppressing symptoms to uncovering hidden drivers. Chronic infections as the hidden root cause of Multiple Sclerosis represent one of the most overlooked contributors to disease progression and disability.

✅ Identify and treat stealth pathogens (EBV, Lyme, Candida)
✅ Heal the gut and support the microbiome
✅ Reboot mitochondrial function and detoxification pathways
✅ Restore hormonal balance and reduce stress
✅ Use nutrition and lifestyle as therapeutic tools

If you’re seeking answers and solutions beyond pharmaceuticals, it’s time to explore a root-cause, functional medicine approach. Work with a knowledgeable practitioner to identify if chronic infections are the hidden root cause of your Multiple Sclerosis—and begin your personalized path to healing today.