Top 6 Autoimmune Triggers You Control: Infections

“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, D.C. & autoimmune-infection expert

To heal from or prevent an autoimmune condition you must identify your body’s unique environmental triggers so you can eliminate them or minimize your exposure.

To recap, the 6 major autoimmune trigger categories can be summarized as F.I.G.H.T.S.™:

Top 6 Autoimmune Triggers: Infections

Growing scientific evidence indicates that chronic infections from bacteria, viruses, parasites and fungi may be the primary environmental trigger for autoimmune disorders.1 According to many holistic 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. My experience corroborates this. In my holistic, Functional Medicine Autoimmune Reversal practice, we find at least one hidden infection 95%+ of the time in clients who seek healing. Most frequently we find Candida, parasites, Lyme co-infections, reactivated EBV, and mycoplasma pneumonia.

Three Short Stories Illustrate the Infection-Autoimmune Connection

Oral Infection Triggers Rheumatoid Arthritis

In this story, renowned immunologist 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 bloodstream 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 needing a 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.

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 and Lyme expert. 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 Lyme co-infections, Martha’s resistant symptoms improved and she felt much better.

Viral and Fungal Infections at the Root of Lupus

After a ten-year history of lupus, aches and pains, a mysterious rash, profound fatigue, and weight loss resistance, Kara signed up for my Functional Medicine Autoimmune Reversal program. Lab work confirmed a fungal infection in her sinuses, candida overgrowth, reactivated EBV, and walking pneumonia. Kara was 100% committed to getting well. She embarked on a 30-day food vacation and discovered that she was sensitive to grains, eggs and nightshades; she modified her lifestyle to be in bed by 9:30 pm; she began meditating and writing in a gratitude journal daily; she took targeted supplements and herbs; and within 5 months, Kara’s symptoms subsided. Within 9 months her lab results improved, her energy returned, her rash vanished, her joint pain diminished, her digestion dramatically improved, and she was finally able to lose 27 pounds of inflammatory weight.

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. 2

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. For a more comprehensive list, check out the Clear Infections chapter in my book, Beat Autoimmune: The 6 Keys to Reverse Your Condition and Reclaim Your Health. Note: If you don’t see your autoimmune disorder listed, Google “[your autoimmune condition] and infections” to explore further. 

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 diabetesCoxsackievirus 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 SyndromeEBV
Systemic lupus erythematosus (SLE)EBV
MyocarditisCB3, CMV, Chlamydia
Hashimoto’s thyroiditis & GravesPorphyromonas Yersinia, EBV
Myasthenia gravisHepatitis C virus (HCV), herpes simplex virus
Guillain-Barré syndromeEBV, CMV, Campylobacter bacteria
Autoimmune urticaria, psoriasis, alopecia areata and Schoenlein-Henoch purpuraHelicobacter pylori (H. pylori)
Celiac Disease, Irritable Bowel Syndrome (IBS), Inflammatory Bowel Disease (IBD), Crohn’s DiseaseSmall Intestinal Bacterial Overgrowth (SIBO)

3 4 5 6 7

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.8 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…

  • 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.9
  • Chronic cytomegalovirus (CMV) – Sjogren’s syndrome
    Chronic cytomegalovirus (CMV) infection can lead to the development of Sjogren’s (SHOW-grins) syndrome. 10
  • 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. 11
  • 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 MS12
  • 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) 13

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.

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 a near-certain chance of having an infection, like Lyme (bacterial infection), Candida albicans (fungal infection), parasites, and/or viral infections too. If you answered YES to any of these questions, keep reading.

Work With a Skilled Holistic/Integrative Practitioner

Infections are a complicated arena for sure, so do what you can to work with a practitioner skilled in finding and resolving infections that underlie autoimmunity, naturally. Titles to look for include integrative, functional or naturopath. If you’re in the U.S. and are ready, willing, and able to dig deeply into your autoimmune root causes and want to resolve them naturally, consider Functional Medicine Consulting with me and my naturopathic doctor-collaborator who specializes in helping to resolve infections and toxins like chronic Lyme, parasites, Candida, and mycotoxins naturally.

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.

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 & K2, vitamin C, a good bioavailable and chelated multivitamin and multi-mineral complex. I take these: multi and minerals.
  • 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, lift 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 the Autoimmune Healing Manifesto. Print it out and post it somewhere where you’ll see it each day for inspiration.

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 hypometabolic, 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.
  • Use 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.

Once you work to clear infections and adopt healthy lifestyle habits, your body can often eliminate many chronic infections on its own. By eliminating the infections, antibody production will lower, autoimmune symptoms will fade, and the immune system will be unburdened to do its job to defend and protect you. That’s a winning strategy to beat autoimmune and thrive.

Take good care!

Image Credit: Bilal O.

P.S: Want my help reversing an autoimmune condition?

If you live in the continental U.S. and are ready, willing, and able to invest in your best health, I offer Functional Medicine Total Health Transformation Programs over Zoom in collaboration with a skilled naturopathic doctor (ND). Get on my calendar for a free 30-minute discovery call.

1 2 3 Infections and autoimmunity: the multifaceted relationship, Sfriso, P., et. al.; March 2010, Journal of Leukocyte Biology, vol. 87 no. 3 385-395, Reference
4 Bacterial Infections and the Pathogenesis of Autoimmune Conditions, G. Sherbet, British Journal of Medical Practitioners, Reference
5 Helicobacter 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., Reference
6 The 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., Reference
7 Epstein–Barr virus, Wikipedia, Reference
8 Jacob Teitelbaum, MD, expert in CFS, fibromyalgia & author of From Fatigued to Fantastic, Reference
9 Jacob Teitlebaum, From Fatigued to Fantastic!
10 Persistent cytomegalovirus infection–the etiology of Sjogren’s syndrome; Burns, JC., Med Hypotheses. 1983 Apr;10(4):451-60. Reference
11 Gut Microbes Linked to Rheumatoid Arthritis, NIH Research Matters, Reference
12 Can Virus Infections Trigger Autoimmune Disease?, Fujinami, RS.,Journal of Autoimmunity (2001) 16, 229–234, Reference
13 Epstein-Barr virus infection induces lupus autoimmunity, Harley, JB, et. al., Bull NYU Hosp Jt Dis. 2006;64(1-2):45-50. Reference




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Palmer is a certified Functional Medicine Health Coach who has helped thousands of people reverse autoimmune conditions based on her own two-decade battle to successfully beat multiple sclerosis (MS). She’s the author of the Amazon #1 bestselling book, Beat Autoimmune, which has a powerful foreword by Functional Medicine pioneer, Mark Hyman, MD.

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