The infection Borrelia Burgdorferi, also known as Lyme disease, was once thought to isolate to the northeastern portion of the United States. It is now known to have spread, and has been diagnosed in the southwestern states, and is now epidemic in parts of Europe and China. Lyme has been a disease of great mystery due to the multiple forms and locations it may hide within the human body. Its effects are wide-ranging, from systemic pain to central nervous system effects, and thus, has been labeled the” great imitator.” Adding to the confusion and difficulty, diagnosis of Lyme disease is not so straightforward. This is probably the reason that modern medicine has failed, and continues to fail, to recognize and treat Lyme disease. In essence, testing of active Lyme disease produces positive results less than half the time.
The inability to accurately assess, and determine the degree of Lyme effects on a single individual, has led to great confusion, even among prominent researchers and clinicians, in how best to treat the disease. Although testing accuracy has improved, Lyme disease is complicated significantly by other immune influencing factors that have, in recent years, just come to light. For example, we now know that ticks, mice, and even mosquitoes are found to carry Lyme disease. In addition, many other infectious agents are co-inhabiting and are passed simultaneously with Lyme disease. These infections include other bacteria, viruses, and even parasites.
Therefore we have two types of Lyme-infected patients presenting in our East Valley Naturopathic Doctors Clinic. Lyme can cause acute symptoms, as can many other infectious agents such as bacteria, virus, parasites, and fungi or yeast. These patients present with new-onset symptoms within days, weeks, and perhaps a few months of exposure to Lyme disease. The other group of patients we most often see have been infected sometime in the past. They may have had some degree of acute symptoms, but they were not sufficient to seek medical help or were misdiagnosed as a mild respiratory infection or Influenza virus. More than 50% of Lyme patients do not recall seeing a bulls-eye rash distinct to acute infections. What can complicate this picture, even more, is that an old infection might have lain dormant for decades, only to be awakened or intensified by a new exposure to mold, viral or bacterial infection.
It is also very likely, as I will explain later, that a combination of viruses, bacteria, fungi, and even parasites having been kept in check, but, due to reasons still too complex for immunology to understand, they have become reactivated. One example is the patient who has a history of Mononucleosis or Epstein-Barr virus (EBV). Epstein -Barr virus causes both mental and physical fatigue, aggravating even mood, and is often confused by many physicians as depression. It might have lain dormant for years, but now with immune suppression, it will reactivate. This has led to the conclusion that many patients with Lyme disease are, in effect, co-infected with other viral, fungal, parasitic, and bacterial infections. We know because we have tested for them. We find in many cases the most severely affected, and most difficult patients to treat, have a combination of all various infections, with the average being 3-5 infections. A Lyme disease treatment program focused only on one area of the possible disease may have some benefit, but will be limited in its total ability to eradicate all symptoms, or the symptoms will return soon after stopping even initial successful protocols.
Historically and currently the treatment of Lyme disease has required the use of antibiotics. The type, dosing schedule, and duration of antibiotics are dependent on the length and type of symptoms present as well as the co-infections, whether from a new or previous exposure. The use of antibiotics produces its own side effects, such as yeast overgrowth, that is part of the underlying problem, and need to be treated and minimized while on long-term antibiotic therapy. Effective Lyme treatment requires effective co-treatment of yeast and candida species overgrowth.
Depending on the duration of a patient’s symptoms, other bodily systems that support energy, mood, and Autonomic Nervous System (ANS) pathways are often affected. Patients often report that though their recovery is much improved, they rarely feel as good as they did before they became ill. We find that other systems, such as the endocrine and neurotransmitter systems (part of the ANS), have to be restored to their optimal function. This requires not just treating all realized and unrealized infections, but evaluating and treating nutrient, hormone, and neurotransmitter deficiencies, which occur as a result of the body’s attempt to function, while being attacked by serious infectious diseases over months and decades.
The diagnostic workup of chronic Lyme and other infectious agents requires reviewing every functioning system in the body including the immune, endocrine, and the neurotransmitter or stress response systems. With good evaluation and treatment protocols, we can eradicate Lyme and other infectious agents, restore optimal functioning of energy and stress response, improve mood, and calm pain pathways, all leading toward a full recovery.
Lyme disease persists as a controversial infection due to its complexity of diagnosis and difficulty in eradication of seemingly persistent symptoms. In addition, even with the CDC’s recent admission that diagnosed Lyme disease cases exceed 300,000 annually, most primary care doctors deny its existence or are reluctant to support patients who desire to be tested. Even if patients are evaluated, many physicians refuse to treat, or offer the standard prescription of the antibiotic doxycycline, that offers very little benefit to the chronically infected.
Treatment is not likely to occur if testing is not done or fails to be sensitive enough to expose antibodies to Borrelia. Diagnosis must sometimes be made by ruling out all other possibilities associated with the patients symptoms and through a comprehensive lab set that includes immune function and possible coinfections and or mold exposures.
Some of the steps listed below may have already been completed by you prior to your diagnosis of Lyme disease, and thus may not need to be in your current program. We want you to feel comfortable with the complexity of the different prescriptions, herbs and protocols, and why we recommend or feel they are important. Not all protocols are required to be completed at once but can be divided over time and prioritized toward your individual concerns and abilities.
With recent updates in genetics, including lab testing of Lyme, coinfections, and mold, we feel we have one of the most comprehensive and effective Lyme treatment protocols in current use today. After 15 years of developing protocols and trying and discovering newer and more effective Lyme and coinfection treatments, we recommend the following 10 step program for optimal eradication and recovery from Lyme disease, coinfections, and mold.
STEP 1. Treat Lyme infection with the Cowden Protocol
STEP 2. Evaluate and treat for mold and biotoxin exposure
STEP 3. Reduce the presence of yeast or Candida species. 
STEP 4. Reduce and eradicate known or suspected parasitic infections.
STEP 5. Reduce overgrowth of bad bacteria within the small intestine. 
STEP 6. Change your diet to reduce inflammatory and immune reactive foods.
STEP 7
STEP 8. Detoxify and boost immune function.
STEP 9. Treat hormone and neurotransmitter deficiencies
STEP 10. Heal your brain with HBOT, FSM therapy, and Neurofeedback. 
