The Truth About Chronic Lyme Disease (And How to Treat It)

Lyme disease is a bacterial illness, one of many infectious diseases, often caused by a black-legged tick, also called a deer tick. When the tick bites, it spreads the Borrelia burgdorferi, or b. burgdorferi, bacteria. While many cases of Lyme disease go away after a short course of antibiotics, many of my patients experience broad, chronic symptoms months or even years after treatment. Though many in the traditional medical community reject the idea of chronic Lyme disease, Functional Medicine finds that many people with long-term symptoms exist, and takes a unique approach to relieving chronic Lyme disease and restoring immune function.

What is the difference between acute and chronic Lyme disease?

Acute Lyme disease is the initial stage of the Borrelia burgdorferi infection that occurs anywhere between 3 to 30 days after a tick bite. (1) Common symptoms include:

• Fatigue
• Flu-like symptoms including fever, hot flashes, and chills
• Joint pain
• Back pain
• Headaches

One of the hallmark signs of acute Lyme disease is the development of a distinctive red, circular rash often resembling a bull’s-eye, known as erythema migrans. However, not everyone with Lyme disease will develop this rash.

When detected right away, acute, early Lyme disease can often be treated successfully with antibiotics like doxycycline, amoxicillin, or cefuroxime. But Lyme disease is notorious for being challenging to diagnose, as these initial symptoms can mimic other common illnesses like the flu and colds, and the hallmark bulls-eye rash doesn’t always appear for everyone. That’s why chronic Lyme disease is often referred to as the “Great Imitator”.

When Lyme disease goes untreated, isn’t treated properly, or doesn’t respond to treatment when it’s first contracted, it can progress to chronic Lyme disease. Also referred to as post-treatment Lyme disease syndrome (PTLDS), it is characterized by symptoms that last for months or years. 

What causes chronic Lyme disease?

The cause of chronic Lyme disease isn’t always clear. If it’s not caught in time and treated properly (and even sometimes when it is), you can experience longer-term symptoms. If you were never diagnosed and treated, or you caught it late after it was in the proper time frame for treatment, then you may have symptoms of chronic Lyme disease. 

Those who were treated with antibiotics may still end up with chronic symptoms. That’s because antibiotics aren’t always effective. In fact, research indicates that up to 10-35% of cases don’t respond to antibiotics (2).

Doxycycline is the antibiotic typically prescribed for the treatment of Lyme disease. When caught in the early stages, about 80% of people respond to antibiotic therapy. (3)

But many don’t respond due to the persistence of the bacteria, which can take the form of spirochetes and cysts, or can hide in biofilms, which are mucosal barriers that the bacteria can live in to evade the antibiotics. Even measures like intravenous therapy, which may involve a long-term antibiotic prescription, don’t always eliminate borreliosis, or Lyme disease. 

The bacteria may also embed so deeply into tissues that antibiotics can’t reach all of it. Furthermore, the bacteria can weaken your immune system, making your body more hospitable and increase the bacterial load in the body. 

LISTEN: Podcast Episode #001 — Overcoming Chronic Lyme with Jedediah Bila

How do you get diagnosed with chronic Lyme disease?

Getting a diagnosis of chronic Lyme disease is difficult due to the fact that it can mimic so many other types of conditions. These include chronic fatigue syndrome, multiple sclerosis, dementia, and fibromyalgia. 

The term post-Lyme disease syndrome was endorsed by many medical organizations and healthcare providers as a term used to describe patients who have ongoing post-treatment symptoms with no objective findings. (4) This label, however, is inaccurate, because it implies that the initial bacterial infection has been resolved, and that any lasting symptoms are the result of other issues, often overlooking complex immunology. 

But with there being no way to test whether Lyme disease has been cleared from the body, a diagnosis of Lyme disease isn’t always possible. 

If you have tested positive via blood tests for the bacteria that causes Lyme disease, you may or may not have been treated with antibiotics. If you still have ongoing symptoms of Lyme disease, you might be suffering from chronic Lyme disease. Keep in mind, if you are tested too early for Lyme disease, your body will not have yet developed an antibody response, so you can still test negative even if you do have it. 

What are the symptoms of chronic Lyme disease?

The main chronic Lyme disease symptoms include:

• Fatigue
• Flu-like symptoms including fever, hot flashes, and chills
• Joint pain and swelling
• Back pain
• Headaches
• Memory problems
• Musculoskeletal pain
• Difficulty concentrating 
• Sleep problems
• Depression and anxiety
• Dizziness and lightheadedness 

READ MORE: The Top Causes Of Chronic Fatigue Syndrome + Exactly How To Reverse It

You may also find that you experience neurology-related symptoms, which means your nervous system has been affected by Lyme disease. These symptoms include facial palsy, radiculopathy, and more. (5)

A Functional Medicine approach to treatment

A Functional Medicine approach to chronic Lyme disease involves multiple facets.

Take A Detailed Health History

We can’t get to the root issue of symptoms of chronic Lyme without a detailed health history. My team and I ask all sorts of questions to understand if it’s possible you’re suffering from chronic Lyme disease. 

Order Comprehensive Labs

The typical labs ordered for Lyme are Elisa and Western Blot. In addition to these, I typically will order 

• CD57+/CD8-Absolute 
• C4a
• C3a
• MSH

CD57+/CD8-Absolute allows us to identify if you might be sick with something other than Lyme, while C4a assesses your immune system to see if you may be affected by Lyme disease. 

I also recommend genetic testing to understand bio-individuality and why a person feels the way they do. Particularly, I look at HLA, or human leukocyte antigens. They’re associated with chronic Lyme symptoms, and we find that about 90% of our patients have at least one gene variant that increases the likelihood of chronic disease symptoms like Lyme. 

Modify Biofilms

A biofilm is a thin film of bacteria that can adhere to surfaces. Though not inherently bad, it’s how bacteria are able to colonize. The composition of the biofilm makes it either pathogenic, in the case of Lyme, or probiotic. 

Biofilm-modifying tools I use include 

• Colostrum and lactoferrin supplements
• Probiotics and prebiotics
• Enzymes
• Stevia
• Xylitol
• EDTA

Address Gut Health

Since most of your immune system lies in your gut, optimizing your microbiome is essential in chronic Lyme disease. We address any underlying dysfunctions like candida overgrowth, which will help strengthen your immunity to fight off infection. 

Support The Immune System

Formulas that will support your immune system include:

• Siberian ginseng
• Samento
• Lysine
• Stevia
• Zinc
• Bee propolis
• Sarsaparilla
• Guaiacum
• Astragalus
• Resveratrol
• Goldenseal
• Grapefruit seed extract
• Cat’s claw

We typically cycle these, so if one bacteria or parasite doesn’t respond to treatment, we can address it in the next round. With this rotational approach, we can address not just Lyme disease, but many co-infections of Lyme disease. 

I’ve put together all of my favorite herbs and supplements for Lyme healing into a collection, which you can look at right here. 

Prescribe Antibiotic Treatment

We recommend antibiotic treatment with doxycycline, amoxicillin, and other antibiotics after the initial tick bite is discovered to treat Lyme disease. But taken alone, we find that a lot of people will need more than just a single round of antibiotic treatment.

Support Genetic Weaknesses

There are certain genes that can predispose you to chronic infections. It’s a good idea to look at MTHFR mutations, which indicate methylation gene changes. If present, we can support the body’s detoxification and methylation pathways. 

Focus On Nutrient Density

When dealing with stealth infections, you must max macro and micro nutrients in their bioavailable form. It’s not one-size-fits-all, and what works at first might need to be changed up over time. There’s a lot of nuance in this topic. 

A good example of this is to look at Alpha-Gal Syndrome, which is common in chronic lyme. It happens from a lone star tick in the United States, and they’re not just found in Connecticut or the Northeast U.S. This condition is caused by a lone star tick, and can cause an allergy to the sugar molecule in different foods. That’s why labs are vital, as they allow us to identify the type of tick. And once the chronic infection is addressed, you can bring those foods back into your diet. 

Additional Therapies For Chronic Lyme

There are many options that people turn to for alternative treatments to chronic Lyme disease. Two that I think are worth considering for some are ozone therapy, and hyperbaric oxygen therapy. 

Hyperbaric oxygen therapy involves entering a pressurized chamber and breathing in 100% pure oxygen. Since your body’s cells require oxygen to function, it stands to reason that a greater concentration of oxygen would accelerate your cells’ ability to regenerate and repair. 

Ozone therapy is another form of treatment involving ozone gas. We breathe in O2 oxygen, which is made up of two oxygen atoms. In ozone gas, the molecules are made up of three oxygen atoms each, making it O3. Ozone is, however, a highly reactive molecule, so it is found to be controversial by many. 

Both therapies, however, have been shown to boost or modulate immune function (6, 7). You may also experience other benefits, such as lowered inflammation from ozone therapy or pain relief from hyperbaric oxygen therapy. (8, 9)

What are co-infections?

There are several co-infections that can occur alongside chronic Lyme disease. I test my patients for these, including

• Epstein-Barr virus
• HSV 1&2
• HHV-6
• Cytomegalovirus (CMV)
• Babesia
• Bartonella
• Rickettsia
• Ehrlichia and Anaplasma

It’s estimated that about 30% of those with chronic Lyme disease also have two or more co-infections. That’s because ticks carry other tick-borne diseases that can be transmitted alongside the borrelia burgdorferi infection. 

By identifying and treating any co-infections, we can remove stress from your immune system. I also provide antiviral support through options like olive leaf, bee propolis, Melissa officinalis, L-lysine, zinc, and Vitamin C, amongst others when appropriate. 

The Link Between Mold And Lyme Disease

One common issue we see in chronic Lyme disease is mold toxicity. This can create a reactivation of Lyme markers, even if you were bitten years ago. Without addressing your mold exposure and decreasing those symptoms, you may not be able to fight off the symptoms of chronic Lyme disease like you otherwise would. 

READ MORE: Are You Predisposed To Lyme Disease And Mold Toxicity?

Controversy and ongoing research

There is plenty of controversy surrounding chronic Lyme disease, with a lack of agreement even on what to call it–post-treatment Lyme disease syndrome, persistent Lyme disease, or chronic Lyme disease. The Centers for Disease Control and Prevention (CDC), for example, doesn’t support the use of the phrase chronic Lyme disease. They do, however, admit that long-term symptoms have a devastating effect on a person’s life, which is a point I can agree with them on! (10) The conventional medicine world simply isn’t giving chronic Lyme disease the attention it needs.  

Regardless of the term used, there are other controversies that surround chronic Lyme disease (11). These include whether antibiotic therapy can fully clear a case of Lyme, and what percentage of those treated do not respond. 

Some clinicians in the traditional healthcare realm feel that chronic Lyme doesn’t even exist. The fact is, many people still are suffering from Lyme disease, even after an initial round of antibiotics. Others didn’t catch the infection early enough to be treated by antibiotics, and they’re still plagued by persistent symptoms.

Bringing it all together

The functional medicine community recognizes the struggles of living with chronic Lyme disease and other forms of chronic illness like autoimmune conditions, and the need for more advocacy. My team and I take a multi-pronged approach to treating chronic Lyme disease, helping you reduce symptoms through a variety of options, including the ones listed in this article. We specialize in uncovering the root cause behind your symptoms, including ruling out or confirming Lyme disease, as symptoms of this condition can look similar to so many other health problems.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.

Photo: unsplash.com

FAQs

Sources

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• Johnson, L., Shapiro, M., Stricker, R. B., Vendrow, J., Haddock, J., & Needell, D. (2020). Antibiotic treatment response in chronic Lyme disease: Why do some patients improve while others do not? Healthcare, 8(4), 383. https://doi.org/10.3390/healthcare8040383
• Zafar, K., Azuama, O. C., & Parveen, N. (2024). Current and emerging approaches for eliminating Borrelia burgdorferi and alleviating persistent Lyme disease symptoms. Frontiers in Microbiology, 15, 1459202. https://doi.org/10.3389/fmicb.2024.1459202
• Wormser, G. P., Dattwyler, R. J., Shapiro, E. D., Halperin, J. J., Steere, A. C., Klempner, M. S., Krause, P. J., Bakken, J. S., Strle, F., Stanek, G., Bockenstedt, L., Fish, D., Dumler, J. S., & Nadelman, R. B. (2006). The clinical assessment, treatment, and prevention of Lyme disease, human granulocytic anaplasmosis, and babesiosis: Clinical practice guidelines by the Infectious Diseases Society of America. Clinical Infectious Diseases, 43(9), 1089–1134. https://doi.org/10.1086/508667
• Theel, E. S., Aguero-Rosenfeld, M. E., Pritt, B., Adem, P. V., & Wormser, G. P. (2019). Limitations and confusing aspects of diagnostic testing for neurologic Lyme disease in the United States. Journal of Clinical Microbiology, 57(1), e01406-18. https://doi.org/10.1128/JCM.01406-18
• Cenci, A., Macchia, I., La Sorsa, V., Sbarigia, C., Di Donna, V., & Pietraforte, D. (2022). Mechanisms of action of ozone therapy in emerging viral diseases: Immunomodulatory effects and therapeutic advantages with reference to SARS-CoV-2. Frontiers in Microbiology, 13, 871645. https://doi.org/10.3389/fmicb.2022.871645
• Gill, A. L., & Bell, C. N. A. (2004). Hyperbaric oxygen: Its uses, mechanisms of action and outcomes. QJM: An International Journal of Medicine, 97(7), 385–395. https://doi.org/10.1093/qjmed/hch074
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• Chen, X., You, J., Ma, H., Zhou, M., & Huang, C. (2023). Efficacy and safety of hyperbaric oxygen therapy for fibromyalgia: A systematic review and meta-analysis. BMJ Open, 13(1), e062322. https://doi.org/10.1136/bmjopen-2022-062322
• Centers for Disease Control and Prevention. (2025, January 31). Chronic symptoms and Lyme disease. https://www.cdc.gov/lyme/signs-symptoms/chronic-symptoms-and-lyme-disease.html
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