Dr. Jemsek’s Innovations in the Treatment of Lyme Disease

Changing the Landscape for Lyme Borreliosis

“By 2002, I had realized how much of a neurologic disease Lyme was; I had to become a neurologist. I soon began using a combination of antiepileptic drugs to control neuropathic pain. That same year, I developed symptom ratings of major clinical categories (such as cognitive functioning, limbic irritability, etc.) that, albeit subjective, helped track clinical progress over time.

“I also knew the role co-infections played in Lyme — especially babesia (a common protozoal co-infection) was a big player! With this in mind, a protocol gradually developed over the years, aiming to purge these infections so the patient could heal their nervous system and the rest of their body. We approached this with a collection of medications, a cocktail that we titrated up slowly to see what was helping and what wasn’t.

“But first we tried to address the stressors that patients had. That’s very important. Equally important was giving patients a treatment they could tolerate: pulsing, taking breaks, and later, enjoying ‘antibiotic holidays.’

“Eventually, we introduced a stabilization protocol, which made a huge difference, making treatment more tolerable for the patient; that is, managing the patient’s POEMS. That’s P for pain, O for addressing their ostracism and alleviating other conditions that act as roadblocks, E for endocrine issues, M for mood stabilization, and S for sleep improvement. Having checked those five boxes, patients would begin the main course of treatment.”

Joseph G. Jemsek, MD, from his memoir

Dr. Jemsek

Other key innovations


He coined the term Lyme borreliosis complex (LBC) as a moniker for persistent Lyme disease, defining it as a polymicrobial infection (with multiple co-pathogens), with multisystem involvement, multicompartmental neurologic manifestations, and immune evasion and immune suppression mechanisms.


Dr. Jemsek recognized T and B immune cell depletion and identified LBC as a co-factor in the expression of multiple chronic illnesses of unknown cause and presented his hypothesis at multiple conferences.


Dr. Jemsek recognized subacute acalculous cholecystitis as a common syndrome affecting patients of all ages with LBC, a diagnostic syndrome not yet in surgical texts.


He developed the concept of a maintenance phase for patients having completed core treatment, in order to lock in immunologic gains.


Influenced by the research and clinical practice of Dr. Robert Bransfield, Dr. Jemsek first emphasized the neuro-anatomical manifestations of LBC and presented on them at ILADS and other conferences. He also introduced the use of IV lactated ringers solution as a major detoxification tool, particularly in patients undergoing an IV-based program.


He began employing sugar alcohols targeting biofilm colonies, with overwhelming clinical evidence that babesia sequesters itself in biofilm throughout the body.


Dr. Jemsek introduced the management of non-hepatic hyperammonemia, with emphasis on reviewing genetic methylation pathways.


He crafted a kefir cocktail recipe to promote gut health, especially in histamine-tolerant patients!


Dr. Jemsek recognized that, late in treatment, approximately 30% of patients with LBC show an immune reconstitution syndrome with migratory arthralgias, dermal flushing, and intensification of neuropsychiatric symptomatology, analogous to the immune reconstitution inflammatory syndrome seen in patients with HIV/AIDS.

He also identified C2/V1 as the origin of the classic cervicofacial headache, often confused with migraine headache.


Dr. Jemsek recognized and defined involuntary weight gain in patients with LBC, indicative of a continued inflammatory state.


Co-authored the design, in collaboration with the Global Lyme Alliance (GLA), of the first clinical study aimed at determining the effectiveness of physician-developed Lyme treatment regimens; a number of patients would be followed over time to monitor a range of microbiological, immunological, genetic, and metabolic assays, to assess clinical improvement.