Clear Infections to Beat Autoimmune


A lot of us have these infections in us. It’s the consequence of our modern-day lifestyles, high stress, poor diets, and environmental toxins. Our immune systems just can’t keep up with it.

– Nikolas Hedberg, Functional Medicine DC & autoimmune-infection expert

One of the first steps in preventing or healing from an autoimmune disorder is to identify your body’s unique environmental triggers so you can eliminate them or minimize your exposure. To recap, the 6 major autoimmune trigger categories are:

Autoimmune Trigger: Infections

Growing scientific evidence indicates that chronic infections from bacteria, viruses, parasites and fungi may be the primary environmental trigger for autoimmune disorders.1Infections and autoimmunity: the multifaceted relationship, Sfriso, P., et. al.; March 2010, Journal of Leukocyte Biology, vol. 87 no. 3 385-395, According to many healthcare practitioners who treat autoimmune conditions, there is almost always a hidden infection that either precedes the initial autoimmune attack or that appears opportunistically when the immune system is weakened.

Three Stories Illustrate the Infection-Autoimmune Connection

1. Oral Bacterial Infection Triggers Rheumatoid Arthritis

In this story, renowned autoimmunologist Aristo Vojdani, PhD, describes the likely trigger of his mother’s rheumatoid arthritis (RA). Mrs. Vojdani went to the dentist with an infection in several teeth. Dr. Vojdani relates what probably followed:

“My mother likely had a Porphyromonas gingivalis or Streptococcus sanguis infection. These are two kinds of oral bacteria that can cause infection. Each of these bacterial strains releases a toxin. The dentist removed the teeth, the barriers were broken, and these toxins got into her blood stream immediately. She started making antibodies [immune system defense] against the toxins and, because of the molecular similarity between the toxin and her joints, her immune cells started attacking her joints. After 5 years, she started having symptoms of rheumatoid arthritis. After another 5 or 10 years, this resulted in complete osteoarthritis, which required total knee replacement.”

While Mrs. Vojdani never healed from the RA, this personal experience motivated Dr. Vojdani to study environmental factors in autoimmunity and eventually develop lab tests to detect early autoimmune reactivity.

2. Lyme Disease Mimics and Exacerbates RA, MS, Hashimoto’s

After many years of conventional treatment for rheumatoid arthritis, multiple sclerosis and Hashimoto’s thyroiditis, Martha, at 64, became a patient of Richard Horowitz, MD, author of Why Can’t I Get Better? Solving the Mystery of Lyme and Chronic Disease. Dr. Horowitz ordered tests for Lyme disease, and they came back positive. “Lyme disease co-infections were mimicking and exacerbating Martha’s [autoimmune] disorders and were responsible for some of her resistant symptoms (i.e., numbness, tingling, joint pain, fatigue and balance issues, etc.).” Once she was treated for the bacterial infections underlying Lyme, she felt much better and her resistant symptoms improved.

3. Bacterial and Fungal Infections at the Root of Lupus

After a 15-year history of lupus, Maria consulted with Michelle Corey, author of The Thyroid Cure and an experienced functional health practitioner. Maria’s health history included a herpes infection, chronic sinusitis, recurrent fungal infections and a bout of walking pneumonia.

Michelle is acutely aware of the potential of infections to induce autoimmune disorders and symptoms, so she sent Maria to specialists who could order the right tests. A rheumatologist found and treated her for an active mycoplasma infection. An ear, nose and throat (ENT) specialist determined that Maria’s sinus infection was caused by a fungus.

Because autoimmune conditions can have multiple roots, Michelle also recommended that Maria do a comprehensive elimination diet to identify potential additional triggers of her symptoms, and suggested adding in nourishing foods and supplements. Within 9 months, Maria’s lab results improved, her rash vanished, her painful joints healed, and her digestion dramatically improved.

Common Infections Can Lead to Autoimmune Disorders

Infections are common throughout our lifetime, but it is actually fairly rare that they lead to an autoimmune disorder. By the time you are 20 it’s likely that you’ve been exposed to or had:

  • Infectious mononucleosis caused by the Epstein-Barr virus (EBV), a.k.a. Herpesvirus 4
  • Cytomegalovirus  (CMV), a.k.a. Herpesvirus 5
  • Human Herpesvirus 6 (HHV6), and
  • Herpes zoster, a.k.a., chicken pox (which can later lead to shingles).

Scientists believe that a variety of factors must usually be present for an infection to result in an autoimmune condition, including a genetic predisposition and other inflammatory lifestyle factors like stress, a SAD diet, poor sleep, leaky gut, etc. 2Infections and autoimmunity: the multifaceted relationship, Sfriso, P., et. al.; March 2010, Journal of Leukocyte Biology, vol. 87 no. 3 385-395,

“No specific infectious agent directly causes autoimmunity. Rather, we see EBV (Epstein Barr Virus) as a co-factor, a common virus that promotes us to be in the condition where the disease can develop.”

– Marc Horwitz, Ph.D., Microbiology & Immunology

According to many healthcare practitioners who treat autoimmune conditions, if patients don’t get better after addressing food triggers and correcting nutrient deficiencies, it’s time to dig deeper and test for hidden infections. These are common infections linked to specific autoimmune disorders. If you don’t see your autoimmune disorder here, Google “[your autoimmune condition] and infections” to explore further. Note that this list is not comprehensive:

Autoimmune Disorder Commonly Linked Infection
Multiple sclerosis (MS) Human herpesvirus 6 (HHV-6), Epstein-Barr virus (EBV aka herpesvirus 4), Rubella, influenza virus, and Human Papilloma Virus (HPV), Chlamydia, Borrelia burgdorferi, and measles virus
Type 1 diabetes Coxsackievirus B4, cytomegalovirus (CMV), mumps virus, and rubella virus
Rheumatoid arthritis (RA) EBV, hepatitis C virus, E-coli bacteria, Citrobacter, Klebsiella, Proteus, Parvovirus, Mycoplasma infection
Sjogren’s Syndrome EBV
Systemic lupus erythematosus (SLE) EBV
Myocarditis CB3, CMV, Chlamydia
Hashimoto’s thyroiditis & Graves Porphyromonas Yersinia, EBV
Myasthenia gravis Hepatitis C virus (HCV), herpes simplex virus
Guillain-Barré syndrome EBV, CMV, Campylobacter bacteria
Autoimmune urticaria, psoriasis, alopecia areata and Schoenlein-Henoch purpura Helicobacter pylori (H. pylori)
Celiac Disease, Irritable Bowel Syndrome (IBS), Inflammatory Bowel Disease (IBD), Crohn’s Disease Small Intestinal Bacterial Overgrowth (SIBO)

3Infections and autoimmunity: the multifaceted relationship, Sfriso, P., et. al.; March 2010, Journal of Leukocyte Biology, vol. 87 no. 3 385-395, 4Bacterial Infections and the Pathogenesis of Autoimmune Conditions, G. Sherbet, British Journal of Medical Practitioners,,  5Helicobacter pylori and skin autoimmune diseases, Mangen, E. et. al., World J Gastroenterol. 2014 Feb 14;20(6):1510-6. doi: 10.3748/wjg.v20.i6.1510., 6The role of Epstein-Barr virus infection in the development of autoimmune thyroid diseases, Janegova, A., et. al., Endokrynol Pol. 2015;66(2):132-6. doi: 10.5603/EP.2015.0020., 7Epstein–Barr virus, Wikipedia,–Barr_virus

These infections usually occur well before – sometimes years before — any symptoms associated with autoimmunity develop, so it can be difficult to make a definitive link between a particular infection and a specific autoimmune disorder.

Infections and Autoimmunity: A Complex Relationship

The relationship between infections and autoimmune diseases is often described as “multifaceted and multidirectional,” involving a multitude of complex actions and reactions in the body.  Although infections may be a trigger for the illness, many infections likely occur and persist due to the illness itself, setting up a vicious cycle of infection and illness.8Jacob Teitelbaum, MD, expert in CFS, fibromyalgia & author of From Fatigued to Fantastic, Infections are opportunistic and often travel together – many autoimmune patients eventually discover that they have multiple bacterial, viral, parasitic and/or fungal infections.

The Science Is In…

Here is a snapshot of research focused on the relationship between infections and autoimmune disorders:

  • icon

    Human herpesvirus (HHV-6) - chronic fatigue syndrome (CFS)

    A study in the Annals of Internal Medicine found that 70% of patients with Chronic Fatigue Syndrome had an active Human Herpesvirus (HHV-6) infection. 9Jacob Teitlebaum, From Fatigued to Fantastic!

  • icon

    Chronic cytomegalovirus (CMV) - Sjogren's syndrome

    Chronic cytomegalovirus (CMV) infection can lead to the development of Sjogren’s (SHOW-grins) syndrome. 10Persistent cytomegalovirus infection–the etiology of Sjogren’s syndrome; Burns, JC., Med Hypotheses. 1983 Apr;10(4):451-60.

  • icon

    Prevotella copri - rheumatoid arthritis (RA)

    In a study of 114 people, a bacterium named Prevotella copri was present in the gut of 75% of people with rheumatoid arthritis (RA) compared to only 21% of healthy control subjects. 11Gut Microbes Linked to Rheumatoid Arthritis, NIH Research Matters,

  • icon

    Upper respiratory viral infections - multiple sclerosis (MS)

    Infections have long been associated with attacks of multiple sclerosis (MS). Several studies found an association between upper respiratory viral infections and exacerbations of MS. 12 Can Virus Infections Trigger Autoimmune Disease?, Fujinami, RS.,Journal of Autoimmunity (2001) 16, 229–234, 

  • icon

    Epstein-Barr virus (EBV) - Systemic lupus erythematosus (SLE or lupus)

    Infection with Epstein-Barr virus (EBV) — best known as the cause of infectious mononucleosis — is an environmental risk factor for Systemic lupus erythematosus (SLE or lupus) 13Epstein-Barr virus infection induces lupus autoimmunity, Harley, JB, et. al., Bull NYU Hosp Jt Dis. 2006;64(1-2):45-50.

5 Steps to Treat & Heal Infections

According to Lee Cowden, MD, board-certified cardiologist, teacher of integrative health, and founder of the Cowden Protocol to treat persistent Lyme, the key to recovery is to strengthen the resistance of the host. Strengthening resistance means getting your immune system in good fighting shape. That entails getting toxins out of the body and adding in nourishing lifestyle practices to optimize your immune system.

  • icon

    Do a Self-Assessment

    Have you ever or do you presently:

    • Been bitten by a tick?
    • Had the mumps, measles, chicken pox, or mono?
    • Had yeast infections?
    • Had oral infections including gingivitis, periodontal disease or infected root canals/implants?
    • Do your gums bleed when you brush them?
    • Had chronic sinus infections?
    • Taken multiple rounds or an extended course of antibiotics?
    • Had sexually transmitted diseases (STDs)?
    • Had travelers’ diarrhea?
    • Had other GI infections: bacteria, fungus, parasites?
    • Run a fever a lot of the time?
    • Have one or more autoimmune conditions or symptoms?*

    *Many experts believe that if you have an autoimmune condition, you also have 100% chance of having an infection, like Lyme (bacterial infection) and/or Candida Albicans (fungal infection) too.  If you answered YES to any of these questions, keep reading.

  • icon

    Find a Holistic/Integrative Practitioner

    An integrative, functional or holistic practitioner will be able to help you get the right tests and offer targeted treatment for your infections. Some practitioners may refer you to a Lyme specialist since chronic Lyme is a complicated arena. To find a Lyme-literate physician, contact either or the International Lyme and Associated Diseases Society. To make sure you get the best lab test results, consider more advanced Lyme testing through iGeneX or MDL labs.

  • icon

    Consider Herbal Anti-Microbials

    Once you’ve gotten the data about any underlying infection, you’re part way to healing. Herbs and natural remedies widely used to help clear infections include monolaurin (derived from coconut oil), oregano extract, olive leaf, wormwood, berberine and silver. And, for Lyme and related co-infections three effective herbal protocols include Beyond Balance, The Buhner Protocol and The Cowden Protocol. Note that it’s important to follow and stick with recommended treatment protocols, which may take months, and ideally with the guidance of an experienced Lyme practitioner.

  • icon

    Adopt Healthy Lifestyle Habits

    • Remove SAD foods: sugar, processed foods, artificial sweeteners and genetically modified foods (GMOs).
    • Add infection-fighting foods: fresh crushed garlic, coconut oil, oregano and fermented foods
    • Supplement strategically: D3, vitamin C, zinc, selenium, Coenzyme Q10 (Co-Q10) and Quercetin.
    • Drink plenty of filtered or spring water to escort toxins out and bring nutrients in.
    • Heal your gut: balance your intestinal flora and seal your leaky gut.
    • Get restorative sleep: 8-10 hours is ideal for anyone with autoimmune issues.
    • Move throughout the day: walk, garden, life weights, swim…
    • Detoxify your home and body: Minimize EMF exposure, use chemical-free home and body-care products.
    • Minimize stress: Eliminate unnecessary stressors and find healthy ways to relax like slow, conscious breathing, yoga, hot Epsom salts baths, laughing, journalling and meditation.

    For a review of the basics, check out our Healing Manifesto. Print it out and post it somewhere where you’ll see it each day for inspiration.

  • icon

    Raise Your Metabolic Rate

    Chronic viral infections – known as “lipid envelope” viruses — are stubborn because they get stored in your fat cells and lodge there indefinitely. To add insult to injury, many people with autoimmune conditions are hypo-metabolic, meaning that their metabolisms are s-l-o-w.

    If you have trouble losing weight, have cold hands and feet, have a lower basal temperature than the standard 98.6F (measured on waking over a week), and/or if you are insulin resistant, then you may be hypometabolic.

    Here are a few tips to get your metabolism up and running:

    • Address any underlying insulin resistance by restricting carbohydrates including sugar, grains, starchy vegetables and fruits.
    • Eat and cook with coconut oil – a natural anti-viral, antifungal, anti-microbial, anti-inflammatory metabolism booster.
    • Get restorative sleep.
    • Reduce your toxic metal burden.
    • Raise your body temperature with exercise – especially high intensity interval training (HIIT) — and saunas.
    • Consider intermittent fasting – eat only during a 6-8-hour window.
    • Breathe deeply, slowly, and intentionally several times per day. Check out Pam Grout’s: Jumpstart Your Metabolism: How To Lose Weight By Changing The Way You Breathe 

Once you address infections and adopt healthy lifestyle habits, your body can often eliminate many chronic infections on its own. By eliminating the infection triggers, antibody production will lower, autoimmune symptoms will likely retreat, and the immune system will calm down.

Take good care!

Image Credit: Aleksandr Markin/iStock