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Autoimmune Diseases & Infections

Dr Auto Immune
March 31, 2023

For a long time we’ve known that bacteria can trigger the immune system in such a way that autoimmune diseases are formed.

Though genes play a role in autoimmune disease, they’re only one piece of the puzzle.

Autoimmune disease (AID) isn’t caused by just one thing. It’s likely that AID happens when someone with a genetic predisposition encounters an environmental trigger — like a bacterial or viral infection.

So let’s take a look at the infection and autoimmune link, common viral and bacterial infections linked to autoimmune disease, and how to test for and care for them.

Bacteria and our Body

Our world is not a sterile one. We are constantly coming into contact with bacteria every second of every day. Most of the time, our body doesn’t detect this bacteria as a problem. It’s learned, through a process called immune tolerance, to recognize which bacteria may kill us, and which bacteria just hangs around.

But it’s not quite that simple.

Most of our immune system is developed by the time we are 2-3 months old. Immune tolerance may start to set in at this time, but it also adapts to our changing environment as our body grows. This is largely due to our microbiome.

The microbiome in a group of organisms (bacteria, viruses, fungi…etc) that live in our body. Mostly in our skin and in the digestive tract. The microbiome in the digestive tract can span all the way from the nose, to the anus. These organisms live with and around us 24/7. Which means that our immune system is constantly coming into contact with them.

When normal immune tolerance occurs, our immune system doesn’t care that most of this bacteria is hanging around. So long as it doesn’t over populate and take over (like SIBO, or intestinal dysbiosis). But for those that are predisposed to autoimmune diseases, certain types of bacteria can be triggering to those conditions.

How do infections cause autoimmune disease?

We are not 100% sure why some bacterial and viral infections trigger one person with an autoimmune disorders but not another. Here are some possibilities:

Some germs look similar to your body’s own cells:

  • Some infectious germs (like viruses and bacteria) have parts that look similar to your body’s own cells. This is called “molecular mimicry.” When your immune system attacks the invader, it also attacks your own cells. For example, the antibodies that your immune system uses to fight off strep throat can also interact with your heart, joints, brain, and skin. This can lead to an autoimmune condition called rheumatic fever.

Some viruses can interfere with how your immune system works:

  • Some viruses may be able to turn off the immune system’s ability to tell the difference between “self” and an “outside invader.” Epstein barr virus (which causes mononucleosis) is a classic example of this.

Infections cause inflammation and damage:

  • Your immune system is good at fighting foreign invaders. But when it attacks, it can also cause inflammation in your body (“bystander effect”). Inflammation can lead to short-term — and long-term — damage to your cells and tissues.


We are continuing to learn about the different bacterial infections and triggers for autoimmunity. Newer research has been identifying specific strains of bacteria associated with conditions we previously didn’t know were associated with infection.

Bacterial infections linked to autoimmune disease:

  • Strep throat
  • Scarlet fever
  • Citrobacter Freundii
  • Methane based bacterial overgrowth
  • Staph Aureus
  • Klebsiella Pneumoniae
  • Enterobacter
  • Morganella Morgani
  • Escherichia
  • Proteus Mirabilis
  • Food poisoning (E. Coli)
  • Lyme disease (co infections)

Fungal infections linked to autoimmune disease:

  • Candida albicans

Viral infections linked to autoimmune disease:

  • Mononucleosis (Epstein barr)

  • COVID-19

  • Cytomegalovirus

  • Measles

  • German measles (Rubella)

  • Hand, foot, and mouth disease

  • Mumps

  • Influenza

  • Zika

  • West Nile

  • Chickenpox (herpes zoster)

  • Parvovirus B19

  • Rotavirus

  • Hepatitis A

  • Hepatitis C

Sexually transmitted infections linked to autoimmune disease:

  • Chlamydia
  • Hepatitis B
  • HSV-1 (herpes)
  • HIV (AIDS)

Addressing Infections to Reverse Autoimmune Disease

Diagnosis and care can be hard for bacterial infections in autoimmunity.

If you suspect an underlying infection may be contributing to your autoimmune condition, a functional medicine practitioner like Dr. Autoimmune can run lab tests for some of the most common pathogens linked to your specific autoimmune condition. We have state of the art testing, including the amazing GI Map!

We look to support infections and also work to relieve stress, detoxify your body, and support your immune system so that it can better defend against these infections without triggering an autoimmune response.

Reversing autoimmunity, especially in complex cases, requires a comprehensive approach that addresses all of your root causes – including infections.

So if you’re ready for root-cause resolution in your own health schedule a consultation with Dr. Autoimmune today by calling us at 303-882-8447 or click here to schedule your appointment.

We’ve set up ‘The Dr. Autoimmune Solution’ which is a comprehensive new patient special that includes a 90 min zoom meeting and everything necessary to determine the root cause of your condition, and start you on the journey to getting your life back.

You’ll get:

  • 90 minute zoom meeting with Dr. Ian Hollaman, DC, MSc, IFMCP aka Dr. Autoimmune
  • A comprehensive case review of symptoms and timelime
  • Review and interpretation of the 90+ marker blood panel (Blood is drawn at least 14 days prior to the appointment at a lab close to you. A blood test kit will be provided by mail.)
  • Evaluation of your case and custom care plan
  • $399 Rate

*This is a Limited Introductory Offer – 1st Time Visitors Only

Also, no matter where you live, you can still receive care from Dr. Autoimmune, because we now offer remote telehealth options so anyone can heal, from anywhere!

Click here to schedule your appointment with us.Don’t forget to follow us on Facebook, Instagram, YouTube and Tik-Tok for more information and tips regarding autoimmune diseases and the functional medicine approach.

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