by Dr. Lisa Ballehr
Chronic complex illnesses are often multisystemic, meaning they involve multiple body systems and are driven by a variety of underlying factors, including chronic infections, immune dysregulation, mitochondrial dysfunction, and environmental toxins. One of the biggest challenges in these patients is chronic indolent infections, which are persistent, slow-growing infections that can go undetected for years while silently driving inflammation, immune suppression, and systemic dysfunction.
What Are Chronic Indolent Infections?
A chronic indolent infection is a slow, persistent infection that may not cause acute symptoms but instead drains the immune system over time, causing low-grade inflammation, immune exhaustion, and multisystem disease. These infections can be bacterial, viral, fungal, or parasitic.
Common Chronic Infections in Complex Illness Patients
📌 Bacterial Infections
- Lyme disease & co-infections (Borrelia burgdorferi, Bartonella, Babesia, Mycoplasma, Anaplasma, Ehrlichia)
- Chronic urinary tract infections (UTIs)
- Small intestinal bacterial overgrowth (SIBO)
- Chronic periodontal infections (H. pylori, Porphyromonas gingivalis)
- Tuberculosis (latent TB), Brucella, Chlamydia pneumoniae
📌 Viral Infections
- Epstein-Barr Virus (EBV) (linked to chronic fatigue syndrome, autoimmunity)
- Cytomegalovirus (CMV)
- Human herpesvirus 6 (HHV-6, HHV-7)
- Enteroviruses (Coxsackievirus, Echovirus, Polio-like viruses)
- Varicella-Zoster Virus (VZV)
- Covid 19
📌 Fungal & Yeast Infections
- Chronic Candida overgrowth
- Mold exposure & mycotoxins (Aspergillus, Stachybotrys, Penicillium, Cladosporium)
- Cryptococcus, Histoplasma, Coccidioides (opportunistic fungal infections)
📌 Parasitic Infections
- Blastocystis hominis, Entamoeba histolytica, Giardia, Cryptosporidium
- Strongyloides, Toxoplasma gondii (brain infections)
Many of these infections are opportunistic, meaning they thrive in weakened immune systems, gut dysbiosis, and chronic inflammatory conditions.
Why Are Chronic Infections Hard to Treat?
🔬 Biofilm Formation: Many chronic infections hide in protective biofilms, making them resistant to antibiotics and antifungals.
🦠 Immune Evasion: Pathogens like EBV, Lyme, and Mycoplasma can suppress or evade the immune system.
⚡ Mitochondrial Dysfunction: Chronic infections drain energy production and promote oxidative stress.
💊 Antibiotic Resistance: Conventional treatment often fails because pathogens develop resistance.
🌍 Environmental Toxins: Heavy metals, mold toxins, and pesticides weaken immune defenses, allowing infections to persist.
Functional Medicine Approach to Chronic Infections
A functional medicine approach goes beyond just “killing the infection”—it strengthens the immune system, reduces inflammation, and restores balance in the body.
1. Identify & Test for Infections
✅ Comprehensive Stool Testing (GI-MAP, Doctor’s Data, or Vibrant Wellness) – Identifies parasites, dysbiosis, fungal overgrowth, and hidden pathogens.
✅ Lyme & Co-Infections Panel (IGeneX, Vibrant Tickborne Panel) – Advanced testing for Lyme, Bartonella, Babesia, Ehrlichia, and Mycoplasma.
✅ Viral Reactivation Testing (EBV, CMV, HHV-6, Coxsackievirus) – Identifies stealth viruses contributing to chronic illness.
✅ Mold & Mycotoxin Testing (RealTime Labs, Great Plains Laboratory) – Checks for mycotoxins from mold exposure.
✅ Organic Acids Test (OAT) – Looks for fungal metabolites, bacterial overgrowth, and mitochondrial dysfunction.
✅ Toxic Metal Testing – Identifies heavy metals that weaken immunity and fuel infections.
2. Strengthen the Immune System
🛡️ Support Immune Modulation:
✔ Medicinal Mushrooms (Reishi, Cordyceps, Turkey Tail, Lion’s Mane) – Balances immune function & reduces inflammation.
✔ Liposomal Glutathione – Supports detoxification & protects immune cells.
✔ Vitamin D3/K2 – Critical for immune defense.
✔ Colostrum & Lactoferrin – Supports gut immunity & protects against viral/bacterial infections.
🌱 Use Herbal Antimicrobials
✔ Oregano Oil, Berberine, Allicin (Garlic extract) – Potent antibacterial & antiparasitic action.
✔ Cat’s Claw, Andrographis, Japanese Knotweed – Powerful against Lyme & co-infections.
✔ Olive Leaf Extract, L-Lysine – Helps suppress EBV & other herpes viruses.
✔ Pau D’Arco, Caprylic Acid – Fights Candida & fungal overgrowth.
3. Break Down Biofilms
Pathogens hide in biofilms, making them harder to eliminate. Biofilm disruptors help expose infections to the immune system.
✔ Lumbrokinase & Nattokinase – Potent fibrinolytic enzymes that break down biofilms.
✔ Serrapeptase & Proteolytic Enzymes – Dissolve protein barriers protecting pathogens.
✔ EDTA & NAC – Helps weaken biofilms & heavy metal detoxification.
4. Detoxify & Support Mitochondria
Infections thrive in toxic, inflamed environments. Supporting detoxification pathways and mitochondria is essential.
🔥 Mitochondrial Support:
✔ CoQ10 & PQQ – Supports ATP production & cellular energy.
✔ Magnesium, Alpha Lipoic Acid (ALA) – Helps with fatigue & neuroprotection.
✔ NAD+ Precursors (NMN, NR) – Supports mitochondrial repair.
🚀 Liver & Lymphatic Detoxification:
✔ Liposomal Glutathione, Milk Thistle, Dandelion Root – Liver detox support.
✔ Infrared Sauna & Dry Brushing – Helps lymphatic drainage & toxin elimination.
✔ Binders (Activated Charcoal, Bentonite Clay, Chlorella, Zeolite) – Absorbs mold, mycotoxins, and heavy metals.
5. Balance the Gut Microbiome
80% of the immune system resides in the gut, and chronic infections are often linked to dysbiosis and leaky gut.
✔ Saccharomyces Boulardii – Fights yeast & supports gut immunity.
✔ Spore-Based Probiotics (MegaSpore, Just Thrive) – Restores microbiome balance.
✔ Bone Broth, Collagen, L-Glutamine – Helps heal the gut lining.
6. Reduce Inflammation & Calm the Nervous System
Chronic infections can trigger neuroinflammation, causing anxiety, depression, and brain fog.
✔ CBD Oil & Omega-3s (DHA/EPA) – Reduces neuroinflammation.
✔ Ashwagandha, Rhodiola, Holy Basil – Adaptogens to lower stress & cortisol.
✔ Mind-Body Practices (Primal Trust, DNRS, Gupta Program) – Retrains the brain & nervous system.
Conclusion: A Comprehensive Healing Plan
🔹 Step 1: Identify the infection with functional medicine testing.
🔹 Step 2: Strengthen the immune system & support mitochondria.
🔹 Step 3: Use herbal antimicrobials & biofilm disruptors.
🔹 Step 4: Detoxify the body from mold, heavy metals, and mycotoxins.
🔹 Step 5: Repair the gut-brain axis & balance the microbiome.
🔹 Step 6: Reduce neuroinflammation & retrain the nervous system.
🔹 Need Help? Dr. Lisa Ballehr specializes in functional medicine for chronic infections and complex illnesses. Book a consultation today to get started on a personalized healing plan! 🚀
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