All About Health
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All About Health

What no doctor told me about antibiotics

What I learned after stopping antibiotic treatments for chronic Lyme disease

A year ago, I was diagnosed with chronic Lyme disease and for the next few months after that, my life revolved around treatment. Or more accurately, it revolved around antibiotics: which to take, at what dosage, IV or oral. Luckily, a lot has changed since then, and I now see that time as the start of a journey learning about chronic illness and healing. But what has continued to surprise me is how many other patients followed a similar trajectory to mine. It seems we all went through the same phases of relief at getting a diagnosis, confusion about what to do next, and the desperation that launched us on a multi-month (multi-year for some) course of antibiotics.

In my mind, I call this time period the medical merry-go-round.

It was the start of cyclical pattern of joy and disappointment as I alternated between rounds of medication and testing. For five months, I took high dosage pulses of multiple antibiotics- doxycycline, tetracycline, and rifampin, to name a few. I had no idea what was going wrong in my body and I was bombarded with conflicting advice and opinions from books, physicians, and other families. Half of those I spoke with told me antibiotics were the only thing strong enough to heal me; the other half told me they would wreck my body for years. The more information I collected, the more confusing the whole picture became. One day about seven months ago, I stepped off the ride and decided to take a more holistic approach to my health. I also had such intense nausea that I knew I couldn’t continue bombarding my own body.

Looking back, if I knew what I now know about chronic illness and antibiotics, I never would have taken more than a single course of treatment. This is what I want to share.

Relief and disappointment: antibiotics and immune suppression

I remember the joy and surprise I felt the first morning after starting antibiotics: my muscle stiffness was gone and it felt good to move for the first time in months. My family and I were thrilled and relieved to be on the right track. So it was all the more painful two weeks later when my supply ran out and my symptoms crept back, making us wonder if I had not taken a high enough dosage or killed enough bacteria. This is what got me- and probably many others- hooked on antibiotics: the joy of symptom relief that goes away once you stop taking them.

What I wish I had known then is that the antibiotics I was taking were suppressing my own immune system. I made the connection many months later when my nutritionist informed me that a change in diet (no dairy, soy, or corn) would clear up most of my symptoms. Within two weeks of the change, the muscular stiffness disappeared and I was able to begin using my hands again; conversely, symptoms returned upon eating any of those foods. As I began to put the pieces together, I realized that similar to the case of a regular fever or infection, the symptoms I experienced were from my own body reacting against both Lyme-related infections and food allergens. The relief I had temporarily experienced was not healing, but a dampening of my body’s ability to even react.

What I had assumed to be progress was more likely the opposite. As a summary of research conducted at Harvard and MIT shared, “the drugs can make the immune system less effective overall: Immune cells called macrophages were found to be less effective at fighting off infection, because the antibiotic choked out their respiration.” Essentially, I was destroying my body’s ability to defend itself and celebrating because I no longer felt the fight it was putting up.

Antibiotics work well for fast-growing bacteria…not slow-growing

Antibiotics are generally tested on bacteria growing rapidly in log phase, and that’s when they are most effective. To be clear, if I am brought to the hospital with an intense and acute bacterial infection, I absolutely want to be treated with antibiotics.

But that’s not how the bacteria associated with Lyme disease or common chronic infections generally behave. Lyme co-infections such as Bartonella are slow-growing, which means there are few of them in the body, they do not divide quickly, and they generally hide within tissues or larger pathogens. As researchers have found, slow-growing bacteria are more difficult to kill. As an older study looking at antibiotic efficacy against slow growing bacteria noted, “For the very slowly growing gram-negative bacteria studied, gentamicin (an aminoglycoside), imipenem (a carbapenem), meropenem (a carbapenem), ciprofloxacin (a fluoroquinolone), and ofloxacin (a fluoroquinolone) exhibited up to 5.7 orders of magnitude more killing than piperacillin or cefotaxime. This is in contrast to optimally growing bacteria, in which a wide variety of antibiotic classes produced 99.9% killing.” Unfortunately, many chronic illnesses involve multiple strains of slow-growing bacteria working synergistically to weaken the body. Antibiotic treatment is not only not very effective against these bacteria, but it causes damage to the very bacteria that support the body’s microbiome and offer protection.

Order of treatment matters

As herbalist and writer Stephen Buhner notes, Lyme pathogens are opportunistic. They gain a foothold in the body when the immune system and/or gut are compromised, and they rarely act alone. A large number of patients with Lyme disease or other chronic illnesses also present with heavy metal toxicity, mycotoxicity (mold), viruses, or a variety of parasites. In my own case, after being treated with two rounds of antibiotics, I discovered I had a fungal and parasitic infection in addition to a Lyme one. One of the biggest challenges for any physician treating a patient then is not just what to do but in what order to do it. When reading through the book, “New Paradigms in Lyme Disease Treatment,” I came across the following section by Dietrich Klinghardt, MD:

“ Other than this, my antimicrobial strategy has always been to treat the creatures in the patient’s body from the largest to the smallest; so that means parasites first, and viruses and nanobacteria, last. This is because parasites are themselves invaded by, and incubate, spirochetes, viruses, bacteria and other microbes. So it makes no sense to treat the Lyme infections and viruses first because the bigger organisms also harbor them, and you won’t be able to fully eliminate them until you eliminate the bigger microbes. Otherwise, you will only be killing the infections and viruses that are outside of these organisms because Lyme-specific treatments do not penetrate into the parasites.”

This type of systemic thinking is unfortunately very rare. Most doctors I consulted were so focused on the bacterial aspect of Lyme disease that they did not look for any other conditions that could be weakening my body before blasting it with antibiotics. As new books and research on Lyme disease emerge, it is clear that bacteria are only one small part of the picture; environmental toxins, opportunistic pathogens, and a weakened body must also be considered before real progress can be made.


A year later, I’m glad to be off antibiotics and I appreciate everything I learned as a result of them about managing my own health.

I still recognize that antibiotics can be incredibly valuable to stem the tide of fast-growing or early stage infections. But as I personally found, in most cases of an illness like chronic Lyme disease, they are unhelpful or even damaging. As the number of chronic illnesses grows, both physicians and patients need to work together to understand the complexity of what is making patients sick and what needs to be treated, and in what order, for them to heal. On a personal level, I hope that in the future, I won’t have to meet as many patients who’ve been on the same merry-go-round of medication and misinformation that I experienced.



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