Lyme Disease: Defining the Controversy, Part II

Lyme Disease Testing

If you’re concerned that chronic Lyme disease might explain your health concerns, then perhaps this story will sound familiar to you:


A few years ago I received a telephone call from Carl. At the age of 66 and following the death of his wife, he had retired from his construction business and accepted a part-time job at Home Depot. He said: “I felt in great shape all summer. Then I caught the flu and felt so awful that no one wanted to be near me. A few weeks later I seized up, felt so stiff and weird inside. When it didn’t go away, I went to my doctor. She diagnosed me with arthritis and gave me pain pills. After a week I didn’t feel any better, so I went back to her and showed her a red spot on my stomach. She said it was a tick, told me I might have Lyme Disease, and gave me antibiotics and a steroid for 3 weeks. It felt awful! 2 months later I was still in so much pain, so I went back and she told me: ‘Well, I don’t know what you have but I know it’s not Lyme Disease. You took antibiotics and your tests came back negative.’” Unfortunately, Carl went on to experience a similar scenario with the Infectious Disease specialist, Rheumatologist, and Internal Medicine specialist. Their message was the same: “Well, I don’t know what you have, but it’s not Lyme.”

I hear similar stories frequently in my office. Sometimes it helps to understand why conventional medical approaches appear to be failing you. Here are at least two main factors, as I see them:


Testing for Lyme disease

In Western medicine, as it is in Western culture, we put a lot of faith in objective evidence. We want that black-and-white answer, the “truth” that’s hidden by natural human bias. This is particularly alluring in a complex illness that mimics many other scary illnesses, including neurodegenerative illnesses and cancer. We want to be sure.

According to some authorities, Lyme disease tests applied by Public Health in most jurisdictions, (referred to as 2-tier testing recommended by the Centers for Disease Control (CDC) in the United States), miss a proper diagnosis up to 50% of the time (1-3). These tests look for immune proteins in the blood (antibodies) as evidence of infection. False negative test results are common for many reasons, including if the test is conducted too early in the disease process, too late after antibody production has dissipated, or following antibiotic treatment. Other reasons for false negative results might be more related to the person’s atypical immune system response, or infection with a less common strain of Borrelia bacteria, or a different co-infection all together. (For a bit more background information, please read some of my other Lyme Disease articles.)

In many parts of the world including Canada, Lyme Disease is considered a “clinical diagnosis”, meaning that we recognize the inadequacy of our technology for diagnosing Lyme disease and the false test results that can occur. Yet Carl’s story underscores how rigidly our mainstream system holds onto the use of these tests as a means of diagnosis. It’s one reason why many people like Carl fall through the cracks.


Antibiotics & Lyme disease

If you experience a flu in the summer time following a tick bite in an endemic area such as KFL&A, you’re automatically considered to have Lyme disease and antibiotics are an effective treatment for perhaps 80 to 90% of people. If someone subsequently develops diverse and debilitating symptoms over months, despite negative test results and with no objective evidence of infection, is it the same illness? If antibiotics don’t resolve this condition, can it still be called “Lyme disease”, since Lyme disease is a bacterial infection? This was the debate that Carl unexpectedly found himself a part of.

Our conventional medical approach offers the logical premise that if Lyme disease is a bacterial infection, and antibiotics fail to resolve the condition, and tests fail to indicate persistent infection, then the patient must not have Lyme disease. Accordingly, a study published in the New England Journal of Medicine in 2001 stopped long-term oral and intravenous antibiotic treatment in patients with chronic symptoms because the antibiotics appeared no better than placebo after 90 days but certainly carried a risk of harm (4). A report released in June 2017 by the Centers for Disease Control highlights the unproven benefit and known risks of long-term antibiotic treatment in chronic Lyme disease (5).  The conclusion from studies such as these is often that persistent symptoms must be due to something else, in which case treating a person in this state with antibiotics is unethical and harmful.

Many “Lyme literate” practitioners counter with good evidence exposing the inadequacy of our antibiotics against such resourceful bacteria. They acknowledge the pleomorphic nature of Borrelia, which means that it changes shape when threatened and more easily evades the immune system. It can burrow into tissues with a little tail (called a flagella) and hide. It can disguise itself as a brand-new bug by creating new proteins on its outer membrane that fool the immune system. These Lyme literate practitioners argue that we need to apply more, not less, antibiotic and in more sophisticated ways to match the cunning of these “stealth pathogens”. Our underestimation of these bacteria is why traditional antibiotic regimes result in a 35% relapse rate of Lyme Disease. So, who’s right?


Lyme disease and your immune system

Whether someone is diagnosed with “chronic Lyme disease” hinges substantially on the assumption that the bacteria must still be present to cause such symptoms. We expect our test results to indicate the presence of the bacterium and we want our antibiotics to kill it. But what if Borrelia was just the trigger for a cascade of other events in the body leading to poorer health, similar to post-COVID syndromes? It could be that dead bacterium continue to trigger inflammatory responses, or that the infection triggered an ongoing autoimmune reaction – we really don’t know. These and many other theories point to underlying concerns of a dysfunctional immune system.

It arguably comes down to this: In acute illness, our immune system reaction is somewhat predictable and antibiotics offer just enough support to enable the body to clean up the mess and restore balance. But after the infection has become established and/or has destroyed various subtle systems in our body, the antibiotics may not be effective and can cause serious damage. Chronic symptoms associated with Lyme illness can be considered as a spectrum disease with varying immune system capacities and dysfunctions. We need to take a more sophisticated view and explore methods that support our body’s ability to restore normal function.

Where do we go from here?

Are you familiar with the phrase “It’s a poor tradesman who blames his tools”? Ultimately, we can’t blame the Lyme disease epidemic on inadequate technologies such as testing and pharmaceuticals. It’s about how we select and employ these tools that’s at fault. What we’re coming to understand is that Lyme disease is less about a single microbial infection and more about the capacity of a patient’s immune system to balance multiple infections at once. Rather than rely on tests that assume a healthy immune response, we need to apply tests that guide us to interventions that support a struggling immune system. In my practice, depending on the person and their symptoms, we’re likely to discuss tests that address the microbiome, metabolism, and digestion, in addition to or as alternatives to technologies designed to identify Lyme disease. And though it can be helpful to have a clear diagnosis, it’s most important to see that people with these chronic symptoms find ways to heal and get their life back.


We can’t solve problems by using the same kind of thinking we used when we created them.” Albert Einstein.



Additional Resources:

For context, please read “Defining the Controversy, Part I

See our self-assessment section for various clinical questionnaires designed to help us determine whether you have Lyme disease.

Review from the Magnotta Research Lab in Guelph, Ontario: Bamm VV, Ko JT, Mainprize IL, Sanderson VP, Wills, MK. Lyme Disease Frontiers: Reconciling Borrelia Biology and Clinical Conundrums. Pathogens. 2019;8(4):299. doi:10.3990/pathogens8040299.

Some additional work by ILADS-associated Physicians:Cameron DJ, Johnson LB, Maloney EL. Evidence assessments and guideline recommendations in Lyme disease: the clinical management of known tick bites, erythema migrans rashes and persistent disease. Expert Review of Anti-infective Therapy. 2014;12(9):1103-1135.


1. Ang CW et al. Large differences between test strategies for the detection of anti-Borrelia antibodies are revealed by comparing eight ELISAs and five immunoblots. Eur J Clin Microbiol Infect Dis. 2011;30(8):1027-32. doi: 10.1007/s10096-011-1157-6.

2. Leeflang MM et al. The diagnostic accuracy of serological tests for Lyme borreliosis in Europe: a systematic review and meta-analysis. BMC Infect Dis. 2016; 25(16):140. doi: 10.1186/s12879-016-1468-4.

3. Waddell LA et al. The Accuracy of Diagnostic Tests for Lyme Disease in Humans, A Systematic Review and Meta-Analysis of North American Research. PLoS One. 2016;11(12):e0168613. doi:10.1371/journal.pone.0168613.

4. Klempner M et al. Two Controlled Trials of Antibiotic Treatment in Patients with Persistent Symptoms and a History of Lyme Disease. N Engl J Med. 2001;345:85-92. doi: 10.1056/NEJM200107123450202.

5. Marzec NS et al. Serious Bacterial Infections Acquired During Treatment of Patients Given a Diagnosis of Chronic Lyme Disease — United States. MMWR Morb Mortal Wkly Rep 2017;66:607–609. doi:/10.15585/mmwr.mm6623a3.


immune system, Lyme disease, Naturopathic medicine

Dr. Sonya Nobbe, ND

Dr. Sonya Nobbe is a Naturopathic Doctor and Director of Kingston Integrated Healthcare Inc. She has been practicing in the Kingston area since 2007. Dr. Sonya maintains a family practice, with a clinical focus on complex chronic disease, including Lyme disease and Fibromyalgia.


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