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Lyme Disease Physicians’ Protocols


By Karen Lee Richards*

The difficulty in treating Lyme disease has led to the development of many different protocols – all with the goal of eradicating the Borrelia burgdorferi spirochete. Most experts have found that an integrative approach, utilizing antibiotics and other natural treatments, seems to have the best chance of success.

Following are summaries of many of the most effective and widely used Lyme protocols, with links to more detailed information. Because Lyme disease is such a complicated illness, self-treating can be dangerous. Regardless what protocol you choose to use, it is best to work closely with your own physician or healthcare practitioner.


Dr. Joseph Burrascano’s Protocol

Joseph Burrascano, MD is one of the most highly respected experts in the Lyme community. He is an internist who practices in East Hampton, NY – a highly endemic area for Lyme disease – and serves as the medical director for Advanced Laboratory Services.

Dr. Burrascano recommends an integrative approach to treating Lyme disease, which includes both antibiotic therapy and supportive therapy such as supplements, diet and non-aerobic exercise.

Antibiotic Therapy – There are four types of antibiotics generally used for treating Lyme disease: tetracyclines, penicillins, cephalosporins and erythromycin. In order to treat chronic Lyme effectively, Dr. Burrascano says a combination of antibiotics is usually required. According to his treatment guidelines, “There is no universally effective antibiotic for treating LB [Lyme Borreliosis]. The choice of medication used and the dosage prescribed will vary for different people based on multiple factors. These include duration and severity of illness, presence of co-infections, immune deficiencies, prior significant immunosuppressant use while infected, age, weight, gastrointestinal function, blood levels achieved, and patient tolerance. Doses found to be effective clinically are often higher than those recommended in older texts.”

Supportive Therapy – Dr. Burrascano considers supportive therapy to be essential in the effective treatment of chronic Lyme. His guidelines list certain absolute rules that must be followed if Lyme symptoms are to be permanently cleared:

  1. Not allowed to get behind in sleep, or become overtired.
  2. No caffeine or other stimulants that may affect depth or duration of sleep, or reduce or eliminate naps.
  3. Absolutely no alcohol!
  4. No smoking at all.
  5. Aggressive exercises are required and should be initiated as soon as possible.
  6. Diet must contain generous quantities of high quality protein and be high in fiber and low in fat and carbohydrates – no simple carbohydrates are allowed. Instead, use those with low glycemic index.
  7. Certain key nutritional supplements should be added.

For specific details of Dr. Burrascano’s treatment guidelines, see: LymeNet.org

Antibiotic therapy is covered on pages 12-22. Supportive therapy (supplements, diet and exercise) is covered on pages 27-35.


Dr. W. Lee Cowden’s Protocol

W. Lee Cowden, MD is a board-certified cardiologist and internist who practices in Phoenix, AZ and is internationally known for his knowledge and skill in practicing and teaching integrative medicine.

Dr. Cowden developed an all-natural treatment approach to treating Lyme disease, which he calls the Cowden Support Program (CSP). His protocol utilizes 14 different Nutramedix products that are taken rotationally.

Two of the six microbial defense herbals included in the CSP, Banderol and Samento, were studied in vitro by Eva Sapi, PhD and her group at the University of New Haven, Connecticut and found to eliminate all forms of Borrelia burgdorferi (spirochetes, round-body forms and biofilm forms). In that same study, the antibiotic doxycycline was not nearly as effective against biofilm and round body forms of Borrelia burgdorferi. In addition to the six microbial defense herbals, the CSP calls for taking six antitoxins plus magnesium to support cellular energy production and normal heart, nerves and brain function and serrapeptase to break down biofilms and fibrin so the immune system can more effectively attack the Lyme spirochetes.

Other important components of the CSP include:

  • Drinking 2-3 liters (or quarts) of water daily.
  • Practicing stress reduction techniques for four minutes before each meal and bedtime.
  • Being in bed resting in a pitch-dark bedroom with minimal electro-magnetic pollution from 11 p.m. to 6 or 7 a.m.
  • Eating more raw, organic foods and avoiding sugars, excessive starches, processed foods, peanut products, canola oil and hydrogenated oils. Avoiding wheat and cow-dairy products as well seems to help.

For a summary of Dr. Cowden’s protocol, see: Cowden Support Program Summary

For details of the full CSP, including nine months worth of checklists you can print out, see: Nutramedix.ec


Dr. Joseph G. Jemsek’s Protocol

Joseph G. Jemsek, MD is a board-certified physician in infectious disease and internal medicine. He operates the Jemsek Specialty Clinic in Washington, DC, which is devoted solely to the treatment of Lyme disease patients.

Dr. Jemsek’s treatment protocol employs long-term cyclic, pulse therapy using antibiotics that are effective against all forms of the organism. Pulse therapy involves the intense use of drugs (in this case antibiotics) on an intermittent basis (for example, every other day, two weeks on and one week off, etc.)

He routinely uses IV clindamycin for advanced neuroborreliosis. He also cycles metronidazole during the treatment period, thereby achieving three separate active modes of treatment (extracellular, intracellular, and cystic). “Since it is very difficult to maintain a patient on such intensive therapy for a prolonged period,” Dr. Jemsek explains, “the rotation of oral antimicrobials through the IV treatment period has been quite helpful in term of program tolerance. In fact, out of tolerance concerns, metronidazole is typically given intermittently and on a short term basis because of its propensity to cause severe Herxheimer reactions, especially in patients with advanced illness.” Dr. Jemsek stresses that the specifics of each protocol will vary because individual patients are given a treatment plan that is best suited for them.

For more details about Dr. Jemsek’s protocol, see: JemsekSpecialty.com


Dr. Dietrich Klinghardt’s Protocol

Dietrich Klinghardt M.D., Ph.D. is a licensed physician who practices in Europe and the United States. (Note: Some of his protocols cannot be used in the United States.) He founded the Klinghardt Academy which provides teachings to the English speaking world on biological interventions and Autonomic Response Testing assessment techniques.

Dr. Klinghardt uses an integrative approach to treating Lyme, combining non-surgical orthopaedic medicine with immunology, endocrinology, toxicology, neural therapy, hypnotherapy and energy psychology.

His biological treatment of Lyme disease, called The Klinghardt Protocol, requires four distinctive steps:

  1. Decreasing toxic body burden/unloading the system – includes improving sleep, eliminating toxins, detecting and resolving interference fields in the body, removing allergenic triggers, removing psychological toxins and removing structural blockages.
  2. Improving disturbed physiology – includes testing for and correcting any deficiencies (hormones, minerals, electrolytes, etc.), adjusting diet, addressing the brain and nervous system environments and exercising.
  3. Decreasing microbial count – treating with ozonated plant oils (rizols). “Rizols have strong and specific anti-microbial properties, no known adverse long-term effects, are relatively inexpensive and are pleasant to take.”
  4. Immune modulation – includes treating immune responses to mold, auto-hemotherapy or auto-urine therapy, Buhner herbs, physics-based immune modulation tools.

In addition to these four steps, he occasionally finds the use of antimicrobials drugs to be beneficial.

For more details about Dr. Klinghardt’s protocol, see: KlinghardtAcademy.com


Drs. Marty Ross and Tara Brooke’s Protocol

Marty Ross, MD and Tara Brooke, ND are experts on the use of integrative medicine to treat chronic Lyme and associated diseases. They practice at their medical clinic, The Healing Arts Partnership, in Seattle, WA.

Drs. Ross and Brooke take an integrative approach to treating Lyme, using advanced holistic and supplement-based approaches mixed with traditional prescriptive medicines.

Their “Successful Treatment Recipe for Chronic Lyme Disease” uses a combination of natural supplements and prescription medicines to address sleep, cytokine control, adaptogens, hormones, essential micronutrients, yeast, Lyme infection treatment, detoxification and co-infection treatments for Bartonella and/or Babesia. In addition, they recommend exercise, other natural medicines for specific problems or symptoms and further steps to consider if adequate improvement is not seen after six to nine months.

For further details about Drs. Ross and Brooke’s protocol, see: TreatLyme.net


Stephen Harrod Buhner’s Protocol

Although Stephen Buhner is not a physician, he is highly respected in the Lyme community and is considered to be an expert on the use of herbal medicine to treat Lyme disease. He was a keynote speaker at the “Lyme and Other Chronic Infections as the Underlying Cause of Chronic Illness” conference hosted by Dr. Dietrich Klinghardt in 2009.

Buhner uses an herbal approach to treating Lyme. Generally he doesn’t approve of antibiotics, but for Lyme disease, he believes they have a place. Because the Lyme spirochete is such a variable and adaptive organism, Buhner believes no single treatment will work for every patient.

The Buhner Protocol is based on four key factors:

  1. The organism uses specific mechanisms, primarily inflammation, to breakdown the collagen tissues in the body in order to generate nutrients so it can live.
  2. Where this breakdown occurs determines where the symptoms emerge.
  3. The organism has the ability to manipulate the immune system of whatever host it is in.
  4. Antibiotics are not very effective for Lyme. Studies show they are only effective about 60% of the time.

Based on these factors, Buhner’s treatment goals, in order of importance, are:

  1. Stop the inflammation that is breaking down the collagen.
  2. Support the formation and strength of collagen in the body.
  3. Design specific treatment interventions based on the individual’s symptoms.
  4. Strengthen immune function.
  5. Use anti-spirochetals to control infection.

For the specifics of Buhner’s protocol for Lyme and co-infections, see: BuhnerHealingLyme.com

For background and an in-depth explanation of Buhner’s protocol, read “From a Source of Profound Insight Comes Hope – A Master’s Update on the Treatment of Lyme Disease”


Other Protocols

Below are additional protocols that could not be summarized here because they require you to become a patient or purchase a book to get information.

Dr. Zhang’s Protocol – Using Chinese medicine to treat Lyme

Dr. Marcus Ettinger’s Protocol – A chiropractor’s natural approach to treating Lyme

Byron White Formulas – Herbal and energetic formulas for treating Lyme (only available through healthcare practitioners)

Last Updated: 5/6/15

* Karen Lee Richards is ProHealth’s Editor-in-Chief. A fibromyalgia patient herself, she co-founded the nonprofit organization now known as the National Fibromyalgia Association (NFA) and served as its vice-president for eight years. She was also the executive editor of Fibromyalgia AWARE, the very first full-color, glossy magazine devoted to FM and other invisible illnesses.  After leaving the NFA, Karen served as the Guide to Fibromyalgia and Chronic Fatigue Syndrome for the New York Times website About.com, and then for eight years as the Chronic Pain Health Guide for The HealthCentral Network.


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