The Connection Between Lyme Disease and Arthritis Joint Pain

The connection between Lyme Disease and arthritis-related joint pain can be confusing even for healthcare practitioners. While people with arthritis alone, or Lyme-related arthritis, experience joint pain, it is important to know what factors are behind arthritis pain to help resolve it. Lyme-related arthritis can result from a lack of early detection of Lyme Disease and treatment, although it can also occur despite treatment.

Before the cause of Lyme Disease was known and treatment was discovered, about 60% of infected individuals presented with arthritis around 4-6 months after experiencing the initial bullet rash known as erythema migrans (EM). Once there was an established connection between EM with Lyme and treatment with antibiotics, the frequency of LA decreased. However, as many individuals do not experience EM or are aware of having had it, Lyme Arthritis (LA) still occurs as a sign of Lyme Disease.

Lyme disease is called “the Great Imitator” because it can be mistaken for health conditions such as autoimmune diseases such lupus and rheumatoid arthritis (RA), Chronic fatigue syndrome, Fibromyalgia, and Multiple sclerosis, all of which are associated with joint pain, as well as thyroid disease and psychiatric disorders among other conditions.

What is Lyme Arthritis?

Lyme Arthritis (LA) is a disease caused by infection with the tickborne spirochete Borrelia burgdorferi. In the United States, Borrelia burgdorferi is the cause of the disease, but there are different forms, called subtypes of B. burgdorferi, which may act differently. Because of this, the typical EM doesn’t occur. Also, co-infections include infectious pathogens that are often transmitted by the tick at the same time as Borrelia. The most common ones include anaplasma, babesia, bartonella, chlamydia, ehrlichia, mycoplasma, and rickettsia.

With early recognition and treatment of Lyme, individuals may never experience LA. It is a late manifestation of Lyme disease, generally occurring 4-6 months after infection. It can also occur in individuals who are treated for Lyme but have post-infectious (refractory) LA, or those who develop another form of inflammatory autoimmune arthritis following Lyme Disease.

Anti-body refractory LA is associated with certain strains of B. burgdorferi and individual factors such as specific genetic DNA polymorphisms, the presence of specific autoantibodies, and a decrease in the ratio of specific immune cells.

Many infectious and autoimmune joint disorders can occur that are associated with Lyme disease. They may be due to an active B. burgdorferi infection in joints, anti-refractory Lyme synovitis, or they may have another form of autoimmune arthritis following Lyme disease. The intracellular form of Lyme disease can trigger RA.

With LA, individuals commonly experience intermittent or recurrent attacks of joint swelling and pain, in one or a few large joints, most commonly the knee. Other large or small joints may also be affected, such as an ankle, shoulder, elbow, or wrist.

What is Autoimmune Arthritis?

Autoimmune arthritis is an inflammatory condition. Generally, it can take 10-20 or more years to develop autoimmune arthritis due to diet and lifestyle factors. Symptoms of autoimmune arthritis often begin slowly and develop over time and can come and go. Symptoms result from inflammation of the joint lining and tissues. RA is a chronic inflammatory disease. It is a chronic condition for which there is currently no known specific root cause or cure.

Typical signs of autoimmune arthritis such as RA include swelling from the synovial tissues of the joints thickening and swelling, stiffness from the inflamed joints that impair movement, especially when first arising or after long rest periods, and pain from the wearing down of cartilage and bone and weakening of surrounding muscles, ligaments, and tendons. Affected joints may appear pink or red, swollen, and feel warm to the touch.

How is Lyme Arthritis Different from Autoimmune Arthritis?

Unlike Lyme disease, the root cause of Rheumatoid Arthritis is unknown. Pain with Lyme arthritis typically involves minimal pain with passive range of motion and unilateral involvement of one or more limited number of joints. Conversely, people with RA often experience bouts of moderate to high levels of pain, called flares, that can be incapacitating and sometimes last months.

A primary difference from LA that has not transitioned to autoimmune arthritis is that it typically occurs in one or more joints, and usually, the affected joint is on one side of the body, whereas autoimmune joint diseases such as RA occur more diffusely, and on both sides of the body symmetrically. Pain in LA is usually in the larger joints, In RA, pain and degeneration happen first in smaller joints such as the fingers, hands, and feet.

With autoimmune arthritis, individuals usually have typical risk factors such as a family history of autoimmunity, or obesity. They are also more likely even if they had EM, to have been treated appropriately with antibiotics and not have developed LA. Therefore, if they have signs of generalized arthritis on both sides of their body (polyarthritis), and have been treated with antibiotics, it is unlikely that they have LA.

Infections and co-infections with Lyme-related bugs can set up inflammation that becomes uncontrolled, destroying the individual’s normal immune response and causing a variety of imbalances within the body’s organs, creating multiple symptoms and diseases. Certain gut pathogens may also be associated with RA, although they may or may not be a cause of the disease.

Because of several issues such as individuals not knowing that they had a tick bite, lack of testing reliability, and delayed diagnosis, it’s not uncommon for joint pain to be initially diagnosed as RA versus Lyme. This can result in ongoing infection and co-infections from what may be Lyme Disease from being diagnosed and treated.

Even though these are basic differences between LA and autoimmune arthritis, it is important to remember that every individual situation is unique. Symptoms may be impacted by pre-existing factors such as other hidden causes of imbalance in the body leading to arthritis, joint pain, and other symptoms or conditions. People with LA may also have an underlying autoimmune disease that is triggered by the course of their Lyme disease or related co-infections. This can make differentiating the two diseases challenging.

Testing and Diagnosis of Lyme versus Autoimmune Arthritis

Misdiagnosis of LA and autoimmune arthritis conditions can happen frequently due to the false negative and false positive results that may occur with the current standard 2-step testing for Lyme Disease. This method that the U.S. CDC currently recommends is a two-test approach in which samples are first tested for antibodies to B. burgdorferi by enzyme-linked immunosorbent assay (ELISA) and those with equivocal or positive results are subsequently tested by Western blotting (WB).

The ELISA is a test that determines if you have antibodies related to certain infectious conditions. These antibodies are proteins that your body produces in response to harmful substances, called antigens. Unfortunately, there are some reasons why a Lyme-infected individual may not show a positive test. For example, it may be too soon after infection for antibodies to be produced, the immune system may be too compromised to recognize the antigen, or the individual may have lost an anti-body response by the time the testing is done.

When the ELISA is positive, the second part of the two-step approach is to do a Western blot test to detects antibodies to several proteins of B. burgdorferi. However, there are many forms of tickborne illness causing disease.

Unlike traditional healthcare providers, functional practitioners often use a PCR test. PCR means polymerase chain reaction. It’s a test to detect genetic material from a specific organism, such as a virus. The test detects the presence of a virus if you have the virus at the time of the test. A PCR test that tests for antibodies for a broad range of antibodies for infection and co-infections associated with Lyme disease helps guide therapy. For example, the Vibrant America Tickborne Panel has a comprehensive antibody (indirect) and DNA (direct) test for the detection of Lyme and co-infections.

While PCR testing may be positive and then become negative post-antibiotic therapy, the persistence of inflammation and arthritic joint pain may continue due to too much inflammation during the infection, infection-induced autoimmunity, and failure to turn down inflammatory responses after eliminating the infection.

RA can also be challenging to diagnose. There is no one blood test used to rule out RA. Doctors typically will physically examine a patient, look for swelling, redness, or warmth in the joints as well as check reflexes and muscle movement. They may also check the blood for the antibodies called rheumatoid factors, anti-cyclic citrullinated peptide antibody, specific proteins such as C-reactive protein (a marker of inflammation), and potentially perform ultrasounds, X-rays, and MRIs.

The reality is that regardless of testing, it may be inconclusive to help differentiate RA from Lyme Disease. With Lyme-related illness, infectious organisms are excellent at hiding in the body. Many of them can create biofilms that they hide in or go dormant, making them virtually undetectable in the blood. This is why it’s important that providers not only test, but also explore the individual’s symptoms, pattern of illness, and address their overall health.

Treatment of Lyme versus Autoimmune Arthritis

Lyme-related arthritis can result in a variety of infectious and autoimmune conditions. While early LA typically requires antibiotic therapy, individuals who do not respond to antibiotics, and are refractory to treatment, may continue to experience the symptoms of LA which can be damaging to the individual’s overall health, and progress to more autoimmune, inflammatory forms.

Unfortunately, there isn’t any single protocol to manage the treatment of either of these conditions. When a person with a history of Lyme Disease experiences arthritis consistent with inflammatory autoimmune arthritis, they likely may benefit from similar treatment to individuals with RA. However, they should always be checked for the presence of an active Lyme-related infection.

Borrelia’s ability to morph between forms may require different treatment approaches. Borrelia can be found in fluid or tissue compartments, extracellular matrix, or intracellularly, making it challenging for successful therapy. Bartonella, a Lyme co-infection is very good at hiding within cells to avoid detection. This is why combination therapy is important. Herbal therapy can enhance the effectiveness of antibiotic therapy. Herbal therapy is also used alone, to treat a variety of infections and co-infections. There are a variety of other natural supplements that can also help manage Lyme-related disease.

Certain types of infections, unrelated to Lyme infection, may also be associated with inflammatory forms of arthritis. For example, certain gut pathogens are associated with RA.  These, too, can be potentially managed with natural herbal therapies. Plants can be powerful anti-viral and anti-bacterial allies in managing infections.

Disease-modifying antirheumatic drugs (DMARDS) have typically been used to manage autoimmune arthritis. Aside from traditional DMARDs, biologic DMARDs, biosimilars, and JAK inhibitor drugs are being used.

Collaboration is important among health professionals.

Traditional medical practitioners usually focus on medication, alone to treat Lyme, RA, or their related symptoms. However, it is important to take a whole-body approach and not just use medication to address these conditions. The root cause(s) of the joint pain may not only be Lyme-related infections. Other contributing factors may be imbalances of hormonal, immune, digestive, detoxification, energy, or neurological systems. Functional practitioners are trained in doing detective work to uncover hidden causes of inflammation with special assessments and lab testing.

Once imbalances in the body are uncovered, functional practitioners should develop a plan which includes diet, rest, exercise, stress management, and supplementation even when a traditional approach of antibiotic therapy is used.

The key reasons professional collaboration is important for arthritis joint pain conditions:

  • Each person is an individual and their bodies may have different pre-existing genetic or other conditions that may be heightened or complicated by a Lyme or RA diagnosis.
  • Functional lab tests can elicit important information to understand hidden clues to metabolic imbalances that may be either caused by Lyme infection, pre-existing imbalances, and opportunities for healing. Each person can benefit from this testing, to get the infection, inflammation, and immune function under control. Traditional doctors do not perform these tests.
  • Correlation of an individual’s symptoms, functional and traditional lab tests with a protocol to rebalance the body is critical to healing. Functional Diagnostic Nutrition Practitioners while they don’t diagnose or treat, are expert detectives in uncovering hidden imbalances in the body, whether they be from hormonal imbalances, infection, digestion, detoxification, energy imbalances, or neurologic issues. Once imbalances are identified, they may refer to other providers, but their unique qualifications help them to recommend a self-healing protocol for their clients to help restore normal function and to decrease symptoms such as chronic joint pain, which may also be accompanied by other symptoms.
  • Other syndromes may be more prevalent in certain conditions which may be beyond a clinician’s expertise. For example, Mast Cell Activation Syndrome is an allergic type of syndrome that results from immune cells called Mast cells, where high histamine results. This occurs with relatively low frequency in RA and with much higher frequency in Lyme disease.
  • Each individual is unique in their response to therapies and their requirements for additional support such as physical therapy, chiropractic, or specialized therapies.
  • Antibiotics used to treat Lyme Disease can disrupt the gut, cause leaky gut, and contribute to the development of new gut pathogens or other body imbalances. Tests to assess for these are typically performed by functional practitioners. While they may be necessary and successful in early Lyme disease to eradicate the disease, rarely are they helpful long term, and with long-term use obliterate the microbiome of the gut and lead to other diseases and occurrence of new symptoms or issues such as a leaky gut, SIBO, brain fog, and other conditions. Some individuals respond very poorly to antibiotics and have significant side effects
  • DMARDs used to treat autoimmune arthritis conditions can decrease immune function. Functional practitioners focus on natural ways to control inflammation and increase immune function through diet, lifestyle, and natural methods.


Distinguishing whether arthritis joint pain is caused by an autoimmune disorder or Lyme-related infection can be challenging. It is critical to understand an individual’s story and course of illness as well as address a holistic plan to resolve inflammation and joint pain, which can significantly impair an individual’s quality of life. Uncovering hidden causes of inflammation and joint pain can be key to developing a personalized plan to rebalance an individual’s immune system and other imbalanced body systems so that they can feel better, move better, and live better.


Buehner, Stephen H. (2015). Natural Treatments for Lyme Coinfections: Anaplasma, Babesia, and Ehrlichia. Healing Arts Press, Rochester, VA.

Buhner, Stephen Harrod. Healing Lyme: Natural Healing of Lyme Borreliosis and the Coinfections Chlamydia and Spotted Fever Rickettsioses. 2nd ed., Raven Press, 2015, p.24.

“Lyme Disease.” Centers for Disease Control and Prevention, Centers for Disease Control and Prevention, 16 Dec. 2019,

Bernard, Quentin, et al. “Borrelia Burgdorferi Protein Interactions Critical for Microbial Persistence in Mammals.” Cellular Microbiology, vol. 21, no. 2, 2018, doi:10.1111/cmi.12885.,bacteria%20in%20this%20autoimmune%20disease.,in%20one%20knee%2C%20for%20example,disease%20rarely%20causes%20symmetrical%20arthritis.

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