Lyme Disease

Lyme disease is on the rise globally,1 yet few physicians and healthcare providers are aware of the magnitude of the problem, let alone understand how to test for and treat it effectively. Those providers who are aware of this complex illness often have a limited understanding of the disease. At the California Center for Functional Medicine (CCFM), we are not only well aware of Lyme disease, but we have extensive experience diagnosing and treating Lyme and other tickborne illnesses.  We have helped thousands of Lyme patients regain their health and lives. If you are struggling with Lyme disease and haven't found solutions elsewhere, you've come to the right place. Read on to learn everything you need to know about Lyme disease and how our unique approach to Lyme disease treatment at CCFM can help you regain your health and return to living a vibrant, full life.

tick on leaf

What is Lyme Disease?

Lyme disease is a multi-system infectious disease caused by the bacterium Borrelia burgdorferi sensu lato. It is transmitted to humans through the bite of an infected tick. In North America, two types of ticks carry Lyme disease:

  • The black-legged tick (Ixodes scapularis), also known as the deer tick, transmits Lyme disease on the East Coast and in the Midwest.
  • The Western black-legged tick (Ixodes pacificus) transmits the disease on the West Coast.
  • Other biting insects may also transmit Lyme disease; however, this concept remains controversial and has not been thoroughly researched.2,3 

Importantly, while Borrelia burgdorferi was the first bacterium implicated in Lyme disease, a growing body of research indicates that other forms of Borrelia can cause a similar illness picture, including Borrelia miyamotoi and Borrelia hermsii. 

Lyme disease has been detected in all 50 states in the USA. In California, Lyme is found in the majority of counties.

In addition to Borrelia, other bacteria, parasites, and viruses can be passed by tick bites. Some of these pathogens include Babesia, Ehrlichia and Anaplasma, Bartonella species, Rickettsia species, Powassan virus, and more.

How Common is it?

While the U.S. CDC estimates that more than 300,000 Americans are infected with Lyme disease each year,4 this number vastly underestimates the actual number of cases due to problems with testing methodologies, rampant misdiagnosis, and underreporting of cases. As human encroachment on natural environments increases and climate change accelerates, Lyme disease's prevalence will only continue to rise.5,6

When was it Discovered?

Early case reports of a mysterious illness that would eventually be recognized as Lyme disease began to emerge along the East Coast of the U.S. in the 1960s and 1970s. It wasn’t until 1975 that the medical community took a serious interest in the disease when a group of people living in the towns of Lyme and Old Lyme, Connecticut, came down with a bizarre assortment of symptoms, including fatigue, arthritis, rashes, and neurological dysfunction.

It was soon realized that the patients had all experienced tick bites before the onset of illness. The black-legged tick was implicated in the spread of the illness, which came to be known as Lyme disease. Several years later, scientist Willy Burgdorfer discovered the infectious cause of the disease, a small spiral-shaped bacterium that he called Borrelia burgdorferi.7

What are the Symptoms?

The symptoms of Lyme disease vary depending on whether the illness is acute or chronic. Many people who experience acute Lyme disease symptoms mistake the symptoms for a summer flu-like illness, leaving the Lyme infection unrecognized.8

Acute Symptoms: 

  • Erythema migrans lesion (aka the “bulls-eye” rash) – Only a minority of people with Lyme disease experience this specific symptom. Furthermore, the rash can take other forms that are not the classic bull’s eye shape
  • Fatigue
  • Headache
  • Day and night sweats
  • Chills
  • Muscle aches and joint pain, this can migrate or move from joint to joint or different body areas
  • Neck pain
  • Sleep issues 

Chronic Symptoms:

The symptoms of chronic Lyme disease are frequently mistaken for other illnesses, such as arthritis or mental illness. 

  • Neuropsychiatric illness, such as depression, anxiety, and suicidality9 
  • Sudden-onset aggressiveness and violence - these symptoms may be more common in people with concomitant Lyme disease and the coinfection Bartonella10
  • Cognitive dysfunction and brain fog
  • Neurodegeneration – Borrelia burgdorferi has been detected in significant quantities in the brains of individuals dying from Alzheimer’s disease11 
  • Insomnia and sleep disturbances, such as frequent waking at night 
  • Neuropathy, particularly numbness and tingling that comes and goes or moves around the body
  • Pain
  • Cardiovascular complications12  
  • Chronic fatigue

Please note that these acute and chronic symptom lists are not exhaustive; there are many other possible symptoms of Lyme disease. One significant problem we run into with chronic Lyme disease is that the symptoms of chronic Lyme mimic those of other chronic illnesses, including fibromyalgia and multiple sclerosis. Fortunately, however, we have an inexpensive, convenient screening tool that can help us differentiate between Lyme disease and other chronic illnesses - the Horowitz MSIDS Questionnaire. 

The Horowitz MSIDS Questionnaire was developed by Dr. Horowitz, a leading clinician, and researcher who specializes in Lyme disease.13 The questionnaire, officially referred to as the “Horowitz Multiple Systemic Infectious Disease Syndrome Questionnaire,” is used to differentiate patients with probable Lyme disease and other tick-borne illnesses from healthy individuals or individuals with non-tick-borne chronic illnesses. While some of the symptoms on the questionnaire can be associated with other illnesses, the HMQ also includes an array of symptoms that Dr. Horowitz identified as being unique to Lyme disease, including:

  • Migratory joint pain
  • Migratory muscle pain
  • Migratory nerve pain 

This scientifically-validated, efficient, and low-cost screening tool can be used to determine if further testing for Lyme disease is warranted. We use the HMQ at CCFM as an initial step for screening new patients, particularly those who present with complex, chronic illnesses of unknown origin. If a patient’s HMQ score suggests possible Lyme disease, we may recommend additional testing. See the “Testing Options for Lyme Disease” section below for more information on the types of tests we use at CCFM for Lyme disease testing. 

This is why working with a Lyme-literate healthcare provider is essential if you suspect you may have Lyme but are uncertain based on indeterminate previous test results and past and present symptoms.

Contrary to What We’ve Been Told, Lyme Disease Can Become Chronic.  

For decades, the medical community believed that Lyme disease was an acute illness that could successfully be treated with a single course of antibiotics. However, the clinical experiences of many physicians suggested otherwise. The concept of late-stage, persistent, or chronic Lyme disease has been around for decades, but only in recent years has a systematic definition been developed. According to ILADS (The International Lyme and Associated Diseases Society), chronic Lyme disease is defined as:14 

"…a multi-system illness with a wide range of symptoms and/or signs that are either continuously or intermittently present for a minimum of six months. The illness is the result of an active and ongoing infection by any of several pathogenic members of the Borrelia burgdorferi sensu lato complex (Bbsl). 

Statistics suggest that approximately 2 million people in the U.S. are affected by chronic Lyme disease as of 2020.15 Lyme disease may become chronic when Borrelia burgdorferi, the causative agent of Lyme, morphs from a free-living form to a “persister" form capable of evading the immune system and of establishing chronic infection.16 Chronic Lyme disease is a real illness with an indisputably significant impact on our collective health. 

How does it Impact the Body?

Borrelia stimulates inflammation

Borrelia burgdorferi infection triggers a systemic inflammatory response, affecting tissues ranging from the brain to the heart. B. burgdorferi has powerful neuroinflammatory effects, triggering inflammation within the brain and central nervous system. Borrelia's neuroinflammatory effects may result in depression, anxiety, brain fog, and other neuropsychiatric symptoms.17,18 

Borrelia burgdorferi may also provoke mast cell activation, playing a potential role in mast cell activation syndrome (MCAS).19 Some of the inflammatory markers most commonly elevated in Lyme disease and MSIDS include C-reactive protein, human transforming growth factor-beta (TGFB1), complement component 3a (C3a), complement component 4a (C4a), and Vascular Endothelial Growth Factor (VEGF).

Interested in learning more about how to manage Lyme-induced inflammation? Check out our article “How to Manage Inflammation in Lyme Disease” for more information. 

Borrelia impairs immune function and may increase the risk of other infections

Borrelia burgdorferi impairs its host's immune function, allowing it to evade the immune system and persist in the body undetected.20 This subsequent immune suppression makes the host more susceptible to opportunistic infections, further harming the body.21 Heavy-handed use of antibiotics for Lyme disease can also disrupt the gut microbiome, accelerating the growth of opportunistic gut microbes such as Candida albicans. This is just one reason why a functional medicine approach, which may combine the judicious use of antibiotics with other non-antibiotic antimicrobial therapies, and gut healing protocols, can be so beneficial.

Borrelia may trigger an autoimmune response

Chronic Lyme disease may also provoke autoimmunity through cross-reactivity between B. burgdorferi antibodies and self-proteins. This mechanism explains why Lyme disease has been linked to multiple sclerosis, rheumatoid arthritis, and Alzheimer's disease.22

Borrelia burgdorferi Doesn’t Travel Alone!  

Lyme coinfections

Ticks contain dozens of microorganisms besides B. burgdorferi, including other types of bacteria, parasites, and viruses. Some of the organisms in ticks are not pathogenic but influence the tick’s ability to harbor and transmit pathogens, making the pathogens in a tick more virulent.23 Other tickborne organisms are pathogenic, causing distinct sets of symptoms and complicating the clinical picture:

  • Babesiosis: Infection with Babesia microti or duncani can cause anxiety, day and night sweats, shortness of breath, and heart racing. 
  • Bartonella: Infection with Bartonella species may cause a sore throat, swollen glands, foot pain, abdominal pain, and pain in large joints such as shoulders and knees. It is also linked to neuropsychiatric disorders such as anxiety, panic disorder, rage, and sudden-onset schizophrenia.24,25 Bartonella is common in cats and other domestic animals and can be transmitted from these animals to humans.26,27 
  • Chlamydia: Chlamydia pneumonia infection causes arthritis, upper respiratory infections, and pneumonia, and may contribute to the development of autoimmune diseases.28 
  • Ehrlichiosis: Ehrlichiosis causes flu-like symptoms, including a dry cough, fatigue, muscle pain, and low white blood cells. It also lowers platelets and elevates liver enzymes. The incidence of Ehrlichia and Anaplasma infections are increasing in the U.S., with most cases occurring among immunocompetent (not immunocompromised) patients.29 
  • Mycoplasma: Mycoplasma pneumoniae over-stimulates B cells, causing autoimmune reactions and rheumatoid diseases, fatigue, and joint and muscle pain. The immune dysfunction triggered by Borrelia burgdorferi makes the body more susceptible to Mycoplasma infection.30,31
  • Rickettsia: Rickettsial infection is frequently mistaken for the flu because it produces symptoms such as fever, nausea, and vomiting. In 50-85 percent of people, it causes a red-spotted rash on the palms of the hands. Like Ehrlichia, it also reduces white blood cells and platelets while elevating AST and ALT. Rickettsia is believed to play a significant but underappreciated role in Lyme pathogenesis, influencing disease persistence.32
  • Viruses: Ticks have also been found to have a high viral density, transmitting novel, harmful viral species such as the Powassan and South Bay viruses.33 

Testing Options

The conventional method of testing for Lyme disease, endorsed by the CDC and Infectious Diseases Society of American (IDSA), calls for a two-tier testing strategy. The first tier is an ELISA (enzyme-linked immunosorbent assay) test, which measures antibodies against Borrelia burgdorferi. The second tier, a Western Blot, tests for antibodies to B. burgdorferi but goes a step further by reporting reactivity to ten different proteins found in the bacterium. However, this two-tier testing strategy poses multiple problems:

  1. The two-tier approach has a low sensitivity (the ability to correctly identify those with the disease) of 30-40 percent in Lyme disease's early stages. This is a pretty abysmal figure! In the later stages of Lyme disease, the sensitivity only increases slightly.34,35  
  2. The two-tier testing approach does not pick up on many naturally-occurring strains of Borrelia that cause disease. Because the Western Blot uses antigens from cultured strains of Borrelia, not clinical specimens, it does not pick up on many disease-causing strains of Borrelia present in our environment, such as Relapsing Fever Borrelia (RFB), Borrelia miyamotoi, and Borrelia bissetti. Recent studies have shown that these pathogens are more prevalent in California and nationwide than was previously appreciated.36,37
  3. The Western Blot is prone to methodological issues. Slight variations in the western blot methodology, including differences in the concentrations of reagents used, can also alter test outcomes and produce false negatives.

What to do when serologic testing is negative, but Lyme is still suspected? 

The problems with the conventional two-tier testing strategy for Lyme disease have initiated the development of new tests from independent labs intended to offer higher sensitivity and specificity.

As the first step in the diagnosis of Lyme, we often recommend serologic tests, including the ELISA, the Western Blot, and the Immunoblot. This new test is more sensitive than the Western Blot and is designed to take its place.38 Serologic Lyme tests can be done through Stony Brook University, Quest, LabCorp, or IGeneX.

If serologic tests come back negative and Lyme is still strongly suspected, we may recommend molecular testing such as the test offered by Global Lyme Diagnostics. The GLD tests antibodies to B. burgdorferi outer surface proteins, expanding the number of species and strains that can be detected.

We may also recommend Elispot T cell activation tests. These tests are run by labs such as InfectoLab and Armin Laboratories, and look at T cell activation for the pathogens. This may be a better indicator of current or recent infection and lead to a more accurate diagnosis. 

However, it is important to remember that the testing for Lyme and other tickborne pathogens is still far from perfect, and we always focus on your individual case and symptoms. Lyme disease is primarily a clinical diagnosis and the tests are used as supportive aids. 

What Differentiates the Conventional and Functional Medicine Approaches to Lyme Disease?

The medical treatment of Lyme disease has become the subject of much controversy. The mainstream medical community argues that Lyme disease is rare and easily treated with a single round of antibiotics. When patients experience symptoms beyond this treatment, they are often dismissed and told that it is not possible that the symptoms could be caused by an ongoing infection, are “post-Lyme syndrome,” or are “all in their head.” 

While conventional, or “allopathic,” medicine is excellent at handling acute medical emergencies and surgery, it falls short in addressing complex, chronic conditions such as Lyme disease. If we compare the field of medicine to a tree, the conventional medical disciplines such as cardiology, neurology, and gastroenterology are akin to the outer leaves and branches of the tree. These disciplines work to control or suppress the outward manifestations of the disease, but often fail to address the root cause of the problem. On the other hand, functional medicine focuses first on the roots and trunk of the tree. A functional medicine doctor addresses the underlying factors that contribute to chronic disease and looks at the body as an interconnected system, rather than a disparate collection of body parts.  

Guided by the research and insights of esteemed scientists and researchers, we recognize that Lyme disease can persist well beyond a single, initial round of antibiotics, causing dysfunction throughout the body. In contrast to the limited interventions offered by conventional medicine for Lyme treatment, functional medicine provides a much broader toolkit, a particularly crucial feature when addressing complicated chronic illnesses such as Lyme disease.

Our Approach to Lyme Disease

Research shows that an array of health variables may confound Lyme disease treatment.39 While the conventional medical model largely ignores the role of these variables, the functional medicine model thoroughly understands the importance of these variables in the context of Lyme disease treatment and recovery. 

Our approach to Lyme disease stands apart from others because we focus not only on supporting your recovery from Lyme disease but on helping you create a strong foundation for sustainable, long-term health. 

Gut Health 

Over 70 percent of the human immune system is located in the gut,40 making gut health an essential element of Lyme disease recovery. Gut support is particularly crucial when antibiotics are being utilized as a component of Lyme treatment. We use a variety of gut-focused testing modalities to assess each patient’s gut health and identify areas for improvement. Strategies for improving gut health may include individualized nutrition and diet interventions, herbal and natural antimicrobial botanicals, probiotics, and prebiotics, and prescription antibiotics when appropriate.  

Hormonal Balance 

Chronic illness takes a toll on the body’s hormonal balance and the stress-response system, also known as the hypothalamic-pituitary-adrenal (HPA) axis. At CCFM, we take a deep dive into each patient's hormonal system and offer various options for improving hormonal balance and stress resiliency, including herbs, nutraceuticals, pharmaceuticals, and nutrition and lifestyle interventions.  


Our modern-day environment exposes us to an unprecedented array of toxins unlike anything humans have witnessed throughout our evolutionary history. Concerningly, a growing body of research indicates that many of these toxins compromise our immune function and provoke inflammation. While our bodies have elegant systems in place for handling toxins, these systems can quickly become overwhelmed by the daily onslaught of toxins in our environment. Left unaddressed, a heavy toxic load can make Lyme disease recovery challenging by impairing our immune systems’ ability to fight infection and exacerbating side effects of treatment. At CCFM, we utilize comprehensive toxin testing and detoxification protocols to identify and address toxic barriers to healing. 

Nutrition for Lyme Recovery

Nutrition is an essential but often overlooked component of Lyme disease recovery. A diet full of processed, refined foods triggers inflammation, and may exacerbate the inflammatory response inLyme disease. Conversely, an anti-inflammatory, nutrient-dense diet is a powerful tool for reducing Lyme-induced inflammation and enhancing immune function, gut health, hormonal balance, and  resilience. 

There’s no one-size-fits-all diet for Lyme disease. Mold illness, mast cell activation disorder, and gastrointestinal issues frequently accompany Lyme disease and may require additional nutrition interventions. Our staff nutritionist, Lindsay Christensen, can help you customize your diet to suit your unique needs and accelerate your Lyme recovery process.    

Stress Management

There’s no doubt about it – living with a chronic illness is stressful.  However, chronic stress takes a toll on your immune system, gut health, and brain, among other systems, creating a vicious cycle that can hinder your treatment. We provide customized recommendations for stress management practices to reduce stress throughout your treatment and instead engage your parasympathetic nervous system, which is involved in the crucial "rest, digest, and repair" response.

Antimicrobial Treatments 

We employ the best of both conventional and functional medicine treatments for Lyme, including judicious use of antibiotics and evidence-backed botanicals with demonstrable effects in Lyme disease. Once your body’s infectious burden is reduced, the immune system can often reestablish proper functioning and become more effective at eradicating harmful microbes on its own. 

Interested in learning more about the antimicrobial treatment options available for Lyme disease? Check out our article “Antimicrobial Treatments” for more information on antimicrobial treatment for Lyme disease and coinfections. 

The Relationship Between Lyme and Mold-Induced Illness

At CCFM, we also look at the relationship between tick-borne infections and toxic environmental exposures, including illnesses induced by toxic mold exposure. Exposure to mold in your living or work environment places a strain on your immune system, distracting it from its crucial task of targeting Borrelia burgdorferi and other infectious organisms. Identifying and treating mold-induced illness may be an essential, pivotal step in your healing journey. Our clinicians have extensive experience treating mold-induced illness and can help you navigate this confusing but crucial aspect of healing. 

Check out our article “The Link Between Mold Illness and Lyme Disease” for more information on how toxic mold exposure interacts with Lyme disease, creating a perfect storm of inflammation, and how treating mold-induced illness can accelerate Lyme disease recovery. 

Brain Retraining

Chronic illnesses, such as Lyme disease and other tick borne infections, significantly impact the brain and nervous system. At a microscopic level, Borrelia burgdorferi induces brain inflammation, with harmful effects on cognitive and emotional health. At a macroscopic level, Lyme disease shifts the body into a chronic state of limbic system activation. The inability to downshift out of this “fight or flight” response into the “rest, digest, and repair” response can significantly hinder the healing process. However, the harmful effects of Lyme disease on brain function and the body’s stress response are not permanent; they can be reduced, and even reversed, by harnessing the power of neuroplasticity.  

Neuroplasticity is defined as the ability of the brain to form and reorganize the synaptic connections between neurons.41 A variety of neuroplasticity-based brain retraining programs, such as DNRS, have been extremely helpful for those recovering from Lyme disease. 

At CCFM, we frequently recommend that patients in recovery from Lyme disease and other tick-borne diseases incorporate brain retraining exercises into their routine. Brain retraining exercises such as DNRS and the Gupta Program help rewire the brain, reversing the adverse neuroplastic changes induced by chronic illness and creating a foundation for healing.

To read more about how you can use brain retraining to aid your healing process, check out our article “Neuroplasticity, Emotional Healing, and Chronic Illness.

Dr. Schweig is amazing. He is a great listener and he addressed all my symptoms and concerns. I feel very confident in his care. He is up to date with the best treatments for my Lyme and co-infections.

Pauline Dyke

You can take control of your health. We can help.

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