How Lyme Disease Affects the Immune System

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Lyme disease is like no other bacterial infection. With most bacterial infections, you expect to take an antibiotic and be over the infection within a week to 10 days. Despite treatment, however, many people with Lyme disease often end up with more serious, widespread infection.

Borrelia burgdorferi: An odd bacterium

The Borrelia burgdorferi spirochete causes most Lyme disease in the United States. At least two other Borrelia species lead to Lyme in the rest of the world. Borrelia burgdorferi is a parasite transmitted by infected ticks from deer, mice, and other small rodents that harbor the spirochete. These animals can have huge numbers of the bacteria and not show any symptoms of disease. Yet when these same spirochetes are transmitted to humans, they cause problems in many organ systems.

Why does the Lyme bacterium affect humans and not the infected animals?

The primary difference is the way the spirochete is transmitted and the way the human immune system reacts to this invader. In humans, the Lyme organism has learned to survive brilliantly.

Evasion starts with invasion

Starting as early as the tick bite itself, Borrelia burgdorferi can evade the best efforts of the immune system in several ways. The tick has certain factors in its saliva that coat the invading spirochetes, protecting them as they enter the body through the skin. This prevents the immune system from “seeing” them. For weeks after a tick bite the immune system of someone infected with Borrelia burgdorferi may not produce antibodies against the bacterium.

Structure is important for evasion

Then there’s the unique feature of Borrelia itself, its flagellum. The flagellum gives the spirochete the ability to cause profound disease. A flagellum is typically an outside tail a bacterium uses to propel itself from place to place. In the Borrelia corkscrew-shaped spirochete, however, the flagellum is located inside the bacteria’s body, somewhat like the skeleton of a snake. The flagellum helps the bacterium invade tissues and thick mucus that would stop most bacteria in their tracks. The flagellum also excites the immune system.  Although the immune system can now see the bacterium, it can’t effectively attack it. Instead it launches a massive inflammatory response that ends up damaging surrounding human tissue rather than killing the bug.

Evasion continues with metamorphosis

Once inside the body, the saliva-protected spirochete also starts to change the proteins on its outer cell wall. The immune system typically uses cell wall proteins to detect a foreign invader, develop specific antibodies to fight it, and mount a coordinated immune attack. But the Borrelia spirochete is like a spy who changes his disguise to blend into the crowd. The police have an initial description of the spy, but it’s no longer accurate.

Lyme symptoms and the immune system

The prolonged immune response, trying to fight Borrelia burgdorferi infection, causes most of the symptoms of Lyme disease, including joint inflammation, skin changes, and neurological problems.

Another aspect of Borrelia burgdorferi is that its changing outer proteins further stimulate the immune system. To return to our spy analogy, it’s as if the police know the spy is disguised and somewhere in the crowd. But because they can’t mount a focused attack, they send all available officers to the scene to destroy everything in the environment. In our analogy, Borrelia burgdorferi is the spy and the officers are immune system cells. The environment, unfortunately, is the tissues of the body.

Immune cells that try to fight the invaders include neutrophils, monocytes, macro-phages, and dendritic cells. None are very effective at clearing the infection, but they do wreak havoc when they are in places like joints. Massive numbers of immune cells that invade the joint tissue take up space and release toxic compounds in an attempt to destroy the spirochetes. These cells (particularly neutrophils) release proteins and small molecules such as cytokines, which further stoke inflammation. The result of all this immune activity is joint pain, inflammation, and persistent arthritis. The same principle operates in virtually all organs affected by Lyme disease.

Borrelia burgdorferi in the brain

In the central nervous system, the story is slightly different. The brain doesn’t have the same immune cells that most other body tissues have. In the brain and spinal cord, the de facto immune system is cells such as astroctyes and microglia. These cells are bad at detecting and eradicating infections. Moreover, they release substances (like quinolinic acid) that can be directly or indirectly toxic to nerves. Similar to elsewhere in the body, they kill human tissue in an effort to kill the spirochete. The infection persists and the brain is damaged as a result of the failed attack.

The unique way that the human immune system responds to the Borrelia spirochete infection causes more problems than it solves. The more that scientists discover about the human immune system and Lyme disease, the better equipped they’ll be to develop treatments that can modulate these painful immune system effects. The ultimate goal of course is reducing or getting rid of Lyme disease altogether.

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208 Responses to “How Lyme Disease Affects the Immune System”

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  1. Brenda R. Says:

    Hi Pam,

    I have been treated for Lymes for 2 years by a Naturopath. I have improved somewhat. My three children have it also! The treatment is very expensive for all of us. Can you make a suggestion on what else I can do for my family and I. We watch our diet…no wheat, no sugar, etc. Thanks!


    • Pam Dodd Says:

      Brenda, watching your diet it great. That should help your bodies fight the Lyme. Indeed, Lyme treatment is expensive. I’ve got no other suggestions for what you can do other than what your naturopath is doing. FYI – many people who use alternative treatments find they also need regular antibiotics to fight the Lyme. Also, most people with Lyme have other co-infections besides Lyme (like Babesia, Bartonella, Ehrlichia, and Anaplasmosis). Have all of you been tested for those? They also need to be treated. Sorry to be the bearer of more bad news but thought you should know, if you don’t already.


  2. Tj Says:

    Anyonr know of Maui Llmd? Lyme not found in Hawaii took one trip to mainland since then I have head pressure and leg weakness… Planning to take immunocal for my
    Immune system to fight ff what’s going


    • Pam Dodd Says:

      TJ, I’m sending HI Lyme info shortly. If you do have Lyme, the Immunocal may not be enough. Thanks for asking.


  3. Karthi M. Says:

    Pam, I am thankful for your research and writing. This blog helps me feel not so alone. After treating my symptoms w/herbs and homeopathic remedies, I am now wondering — do you feel it’s absolutely necessary to do long term antibiotic treatment to be rid of Lyme? I’m probably at Stage 2.. maybe 3. Have you ever heard of someone being freed of Lyme w/o antibiotics? The only reason I ask is that I grew up w/doctors and was severely overmedicated all through childhood so I am nervous about my immune system being weakened.


    • Pam Dodd Says:

      Karthi, while I don’t personally know anyone who has gotten rid of Lyme with just herbs and naturopathic remedies, after 6 years of antibiotics myself, I’ve just begun an vibrational/herbal protocol that reportedly has helped others with Lyme get rid of it without pharmaceutical drugs. It’s too soon for me to say if this is what finally chases my numerous Lyme-related infections away for good. But you might want to check out Thanks for asking.


  4. Kathy Says:

    Greetings. Last summer I had a very large rash on my leg (not bullseye) after an apparent bite but never found a tick. My doctor treated me for Lyme with doxycycline (3 weeks) and I later tested negative (twice). I had found numerous small ticks on my person prior to that but none embedded. I am now having hip and soft tissue pain, tingling below both knees, and occasional dizziness. I am awaiting blood test results for autoimmune disorders. I found your blog and was wondering if you can recommend a Lyme doctor in the Gainesville/Fairfax, Virginia area. Thank you!


  5. Anna Says:

    My 13 year old son is suffering from many of the symptoms listed. He has been to many doctors and they can’t find out what’s wrong. A naturopathic PHD told us he had “positive Lyme protein bands.” He has been out of school since December.

    Could you suggest an LLMD in Minnesota? Thanks!!!!!


  6. Megan Says:

    Hi, I live in Central FL and see an integrative medicine specialist who highly suspects Lyme or co-infections. I’ve been tested with the standard tests, which were negative, except for some oddities/elevations in Band 41 of the test. I have high inflammation, tested positive for CMV, EBV & HHV-6. Recently diagnosed with severe carpal tunnel, trigger thumb and have nerve pain in feet. Diagnosed with Fibromyalgia & Chronic Fatigue years and years ago. The past 3-5 yrs I’ve had bouts of swollen glands, severe allergic reactions (never determined to what), weeks of extreme fatigue, etc. Now dealing with unexplained hair loss, tense and tight muscles, anemia, low Vit D, poor concentration…I’m at the point of deciding to do the IGENX tests (which are terribly expensive). I honestly think I need to see a specialist who can explain how Lyme could be possible so I can inform my husband who is not willing to believe it. We live in an area that has deer around and is very wooded, so I’m sure its possible. I’d love some names or a referral to an infectious disease or other doctor who can help me sort this out. Thank you.


  7. Jessie Says:

    Oct. 2010 I started to experience dizzy spells and headaches. They got progressively more intense and more frequent. Progressed to hearing difficulties, ear pain and suddenly plagued with 4 ear infections back to back. I hadn’t had an ear infection since childhood and am now in my mid 30’s. ENT put a tube in my ear, then discovered a mass in my nasopharynx. With surgery in April to remove the “mass” (was not cancerous) I thought it was all behind me. Then June of 2011 I had a red rash (the rash changed over time and only appeared to have the classic bulls eye for a brief period of time) At 1st the nurse practioner said it was dermititis and wanted me to follow up in a week or so. A few days after my initial visit I ended up in the ER for severe nerve pain radiating down my left arm. It had started gradual and became unbearable within 2-3 days. I left the hospital that night with a diagnosis of shingles and an extensive list of medications to treat shingles. At my next follow up and a few days into the shingles treatment, I brought up my concern about lymes. She ordered a test. I got a call with the results as I sat in the waiting room of yet another hospital after a different nurse practioner referred me there out of concern for the pain I felt radiating down my arm and chest. I received confirmation that the initial test came back positive and I began treatment with antibiotics. They advised me that there was a 2nd test they wanted to order which also came back positive. I thought the worse was behind me until a few days later I was back in the ER with the worse headache I have ever had and bp of 189/101 ( Normally I have no issues with my bp) After more blood work and a spinal tap, showed positive still for lymes and NOW bacterial meningitis (they said it wasn’t the kind related to lymes, just a coincidence). After treatment a visit to the infectious disease specialist and several months symptom free I began to get those dizzy spells and headaches again. Followed by joint pain that comes and goes at varying intensities, severe short term memory loss, spells of extreme fatigue lasting weeks at a time, tingling on right side of my head and a finger that seems to lock in the bent position. I feel like I am back on the roller coaster again. I don’t know if everything from the beginning was related to the lymes, but I certainly don’t want to have to suffer through 8 months trying to figure out whats going on. Lymes was the only diagnosis made based on blood work. The rest was based off of my symptoms. I’ve got an appointment set for a neurologist in a few weeks, but don’t know if this relates to lymes and would really like to set up something with an LLMD as soon as possible. I live in Southern Maryland. Can you suggest someone for me? Thanks so much.


    • Pam Dodd Says:

      Jessie, I’d see a Lyme specialist who knows how to diagnose Lyme correctly and treat it adequately if you have it. Most neurologists, rheumatologists, and even Infectious disease specialists know little about Lyme. Continuing on a “treat-the-symptoms” wild goose chase is frustrating, tiring, and expensive. You could also have one or more of the co-infections that typically come with Lyme (Babesia, Bartonella, Ehrlichia, and Anaplasmosis) and need to be tested for those too.

      I’m sending you Maryland Lyme info shortly. Thanks for asking.


  8. Christine Says:

    I was bitten a few times but the bite I remember most was on the side of my neck over a year ago. No bull’s-eye but my lymph nodes on that side were huge for several weeks. I went to the doctor who told me that he himself had been bitten many times and he did not have Lyme. Needless to say I was never tested. My neck has been so stiff I have needed to help lift my head off the pillow with my arm. I have tingling and numbness on both sides of my face. Both arms and legs have felt weak and numb. Stomach pain, fatigue, anxiety from thinking I am terminally ill or have a brain tumor because I feel so awful. Severe vertigo muscle fatigue, tiredness,and back pain that happens in a different part of my spine everyday. I went to a orthopedic Dr who did a Mri of my neck and is now sending me to a neuroligist in a couple of weeks. The Mri showed mild arthritis, no pinched nerve. I am going to ask for a Lyme test.


    • Pam Dodd Says:

      Christine, tell me where you live and I’ll send you info on how to find a doctor who knows how to diagnose Lyme correctly and treat it adequately if you have. Most people with Lyme also have at least one co-infection (Babesia, Bartonella, Ehrlichia, or Anaplasmosis), which also need to be tested for and treated. Most regular doctors use the CDC ELISA test for Lyme, which is very unreliable, reporting a lot of false negatives. Also sorry to say, most orthopedists, neurologists, and rheumatologists know little or nothing about Lyme. Thanks for asking.


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