Chronic Lyme Part 3: Treatment Considerations

Chronic Lyme disease is an extremely complex illness. Once it has been diagnosed, the next challenge is understanding how to treat it. In this article, we will touch upon conventional antibiotic therapies used to treat Lyme borreliosis and its associated coinfections, as well as discuss general approaches for how best to support patients toward remission. Botanical therapies can also play a critical role in the treatment process. Understanding their advantages can assist in choosing the best therapeutic approach. Biocidin® has conducted in vitro research showing a pronounced effect against Borrelia in all of its forms.

Antibiotic Considerations

One of the main considerations when using antibiotics is the fact that Borrelia, based on the environment, has different pleomorphic forms it can select – spirochete, cell-wall deficient form, cyst form/round bodies. For this reason, multiple antibiotics are needed to appropriately treat each form and its location, intracellular and extracellular. Some of the major groups of medications that are used include macrolides (tetracyclines and erythromycin), which target bacterial ribosomes and are used for intracellular cell-wall deficient forms. Penicillins and cephalosporins that target cell walls are best for extracellular spirochetes. And some medications target cyst forms of Borrelia such as metronidazole, tinidazole, and Plaquenil (hydroxychloroquine) (1). The choice of medications and dosages used will differ from person to person based on duration and severity of the illness, as well as the presence of coinfections and opportunistic infections, immune deficiencies, gut health, weight, age, and tolerance (2).


The most common antibiotic recommended for any Lyme presentation is the tetracycline Doxycycline, with its ability to address intracellular, cell-wall deficient forms of Lyme. The CDC recommends dosing at 100 mg twice daily for 10 to 14 days for early or acute Lyme borreliosis and up to 28 days for more disseminated Lyme (3). According to ILADS – the International Lyme and Associated Diseases Society made up of Lyme-literate experts – this dose and duration are not enough to eradicate Borrelia. This dose is bacteriostatic (4) rather than bactericidal, and large spikes in blood and tissue levels show more bactericidal activity. Thus Doxycycline prescribed at 200 mg 2x/day is more effective against Lyme borreliosis (2).

Doxycycline has side effects that should be monitored. First, it can create photosensitivity resulting in severe sunburns. Patients should be directed to stay out of the sun while on this medication. It also often leads to GI distress and the inability to tolerate the medication, especially at higher doses.

For initial treatment of early Lyme with erythema migrans (EM) presentation, ILADS recommends Doxycycline be used for at least four to six weeks, often alongside other first-line antibiotics and those that target cyst form (5). Treated immediately and aggressively, acute Lyme can be successfully resolved, and when an EM rash is present, waiting for laboratory confirmation to treat is not recommended (2).

In chronic Lyme, continuous treatment should be administered until the active infection has been cleared. This typically requires a minimum of four to six months and often much longer (2). Additional classes of antibiotics are strongly suggested to address the cyst and spirochete forms of Lyme and other possible coinfections. Doxycycline has been shown to be effective where Anaplasma or Ehrlichia are also possibilities.

For more information on antibiotic treatments for addressing Borrelia please visit Dr. Burrascano’s Treatment Guidelines For Lyme And Other Tick-Borne Illnesses.

General Principles in Addressing Chronic Lyme Disease

Chronic Lyme disease affects every system in the body. The biggest challenge is knowing where to start when it comes to treatment. Using a holistic and integrative approach is critical not only for reducing the bacterial load but also for strengthening and supporting each system. No one protocol fits all, and individual circumstances such as comorbidities, coinfections, and opportunistic infections, heavy metals, mold toxicity, methylation defects, and chronic inflammatory states must be taken into consideration when developing a treatment plan.

The sole purpose of antibiotics is to kill the infection. Although this is an important part of treating chronic Lyme disease, focusing on “killing” alone is not enough. These bugs are very good at evading our immune systems and antimicrobial agents, so focusing solely on killing the infection can be ineffective. The general principles in addressing chronic Lyme disease, which should be prioritized, include supporting detoxification pathways, reducing inflammation, immune modulation, and, of course, using antimicrobial agents.


Detoxification is key to help reduce Herxheimer (Herx) reactions that occur when using antimicrobials. As the Borrelia and coinfections are killed, they release toxins and neurotoxins that can make symptoms worse before they improve (6). Often, Herx reactions are so intense that patients cannot continue antimicrobial treatments. Therefore, it is key to start protocols with some sort of detoxification support. Many Lyme patients also suffer from already impaired detoxification pathways that may be affected by genetic SNPs, toxins, and heavy metals (even mycotoxins) from mold. Pushing ahead with protocols without properly supporting detox pathways will often set patients back. It is critical to allow enough time to work on detox and drainage before introducing antimicrobial protocols and to continue them through the entirety of their treatment. When addressing detoxification, make sure to consider all major emunctories including liver, kidneys, lungs, colon, lymph, and skin.


Glutathione is a potent antioxidant made up of the three amino acids: cysteine, glutamine, and glycine. It is produced in the liver and targets reactive oxygen species. It is known to be neuroprotective as it prevents neuronal death associated with amyloid plaque deposits (7). This is a useful nutrient for detoxification as well as for supporting brain function and can be valuable for those who also suffer from mycotoxin illness.

Smilax glabra

Smilax glabra is an excellent herb for supporting detoxification and inflammation. The polysaccharides contained in the rhizomes have been shown to reduce nitric oxide, TNF-alpha, and IL-6, thus modulating inflammatory response. Unlike the other species of Smilax, this form can cross the bloodbrain barrier, giving it the ability to neutralize neurotoxins and play a significant role in mitigating Herx reactions, particularly where they include the worsening of neurological symptoms (8).

Other Supportive Detoxification Botanicals and Practices

Other botanicals that can support detoxification include milk thistle, dandelion root, burdock root, and schisandra, as well as aloe for supporting the colon, juniper berry for the kidneys, and cleavers for the lymphatic system. In addition to botanicals and nutrients, patients can incorporate at-home practices such as dry brushing the skin for supporting the movement of lymph, castor oil packs over the liver, Epsom salt baths for supporting detoxification and relaxation of the muscles, and full-spectrum infrared sauna for those who have access. Many Lyme patients are particularly sensitive to detoxification. These patients can use homeopathic drainage remedies that focus on liver, kidney, and lymph drainage to open emunctories. Finally, binders such as Biocidin’s G.I. Detox™+, which includes activated charcoal, zeolite clay, and silica, help absorb and eliminate the toxins that are circulating. Because it is extremely important to mitigate Herx reactions, G.I. Detox™+, is often given to patients early in the protocol for optimal support.


Those with chronic Lyme disease suffer from immense amounts of systemic inflammation, with additional inflammation triggered by the Herx reactions. This inflammation causes many of the symptoms these patients experience including joint and muscle pain, nerve pain, cognitive dysfunction, GI distress, and even inflammation of the lining of the heart and brain (6).

Where does all this inflammation come from? Borrelia stimulates cytokine production through two mechanisms, directly by creating the cytokines and indirectly by stimulating the body’s cytokine responses to the infection (9). Borrelia morphs to and from different forms and changes its outer protein surface markers, confusing the immune system. As the spirochetes cause tissue breakdown, these tissue fragments, along with fragments of dead spirochetes, create an autoimmune-like reaction in which the immune system starts to attack similar structures in the body (9). Spirochetes are also extremely fast. They have two “motors” which increase their motile power and allow them to easily escape the body’s slower-moving white blood cells, enabling them to colonize throughout the body. This explains the hallmark migratory pain that many Lyme patients experience. To get ahead of the symptoms, the inflammatory response must be addressed to reduce the cytokine storms and support a more balanced response from the immune system.


Curcumin is a compound found in turmeric and is a useful anti-inflammatory agent. It also has strong antioxidant capabilities and is immune balancing. Curcumin is neuroprotective and promotes neuroregeneration by increasing neuron stem cell growth in the brain up to 80% (10).

Red Sage (Salvia miltiorrhiza)

Red sage can normalize cytokine responses to microbial infections, in particular regulating unhealthy NF-kB behavior which is one of the primary pathways activated by Borrelia (11). It is often used in combination with Chinese skullcap.

Chinese Skullcap (Scutellaria baicalensis)

Chinese skullcap is one of the strongest cytokine-modulating herbs and is useful against the entire Lyme group of stealth pathogens. It has wide systemic absorption, is protective of endothelial and epithelial cell damage caused by intracellular cytokines, and is indirectly antibacterial as it blocks the ability of the bacteria to scavenge nutrients from the host cells, making it hard for the bacteria to survive (11). These cytokine-modulating herbs can reduce the severity of infection and protect cellular and organ health, making them a critical part of Lyme and coinfection treatment.

Immune Modulation

Although resolving infection is the ultimate goal, we have come to understand that because Borrelia has been shown to lower immune responses, a more realistic approach is to reduce the bacterial load to a threshold the immune system can handle on its own. This requires supporting immune function so it can appropriately respond to fight the infection. Because the gut harbors 70-80% of our immune system, it is key to address gut health in supporting immune function. Many immune-modulating botanicals have the bonus activity of supporting gut health.


Cordyceps is highly protective of sphingomyelin (lipids of the myelin sheath), the lungs, brain, and kidneys. It is a strong inhibitor of hydrogen-peroxide oxidation and LPS in microglia cells. It inhibits production of NO, PGE2, and proinflammatory cytokines and actively protects the mitochondria from ROS. Cordyceps modulates immune responses intracellularly which is key when addressing an intracellular infection. To be effective, it must be viewed as a medical food and dosed with a minimum of three grams daily, but six grams daily is ideal as a baseline (11).


Another potent immune modulator is astragalus. It works by supporting several facets of the immune system, including enhancing phagocytic activity of monocytes and macrophages, increasing interferon production and natural killer-cell activity, enhancing T-cell activity, and potentiating other antiviral mechanisms. It is particularly useful in endemic areas to help prevent Lyme disease as it counteracts immune suppression caused by saliva-inhibition factors of ticks. It should be noted that in patients with late-stage Lyme disease, astragalus may exacerbate autoimmune responses, while in others it alters Th1/Th2 balance and reduces autoimmune dynamics, so patients should be monitored when astragalus is used (12).

Treat the Gut with Biocidin® Liquid Formula

When it comes to the gut, factors such as diet and nutrition, increased permeability, overgrowth of yeast and bacteria, and microbial abundance and diversity must all be taken into account. Biocidin® Liquid is a proprietary blend of 17 botanical extracts and essential oils which give it broad-spectrum antimicrobial capabilities as well as immune-modulating properties. Biocidin capitalizes on the synergy of combining different herbs in a formula, as opposed to a single botanical, which results in a layering effect with a greater breadth of activity.

Along with Biocidin®, the probiotic formula Proflora®4R can be used to address the dysbiosis often seen in Lyme patients. Proflora®4R contains spored-based probiotics with quercetin for addressing tight junctions and lowering histamines. For additional support, L-glutamine or serum-derived immunoglobulins can be used. Once health has been restored in the GI tract, it is helpful to graduate to Biocidin®LSF, a liposomal formula, for enhanced intracellular and systemic delivery.

Antimicrobial Herbs

Herbal options provide a powerful way to address chronic Lyme and coinfections. They often have broad-acting mechanisms of action, fewer side effects, more support for overall vitality, and, due to their many constituents, less microbial resistance than conventionally used antibiotics.

Teasel Root (Dipsacus sylvestris)

Teasel root is considered a valuable antimicrobial and anti-inflammatory herb in the treatment of Lyme disease. Some sources believe that it helps to bring spirochetes into the bloodstream from the tissues, making them more vulnerable to antimicrobials. In particular, teasel root is very supportive in addressing Lyme arthritis. It can cause significant Herx reactions at the start of treatment but dropping the dose is typically all that is needed to reduce the reaction (10-30 drops daily) (6).

Cat’s Claw (Samento) (Uncaria tomentosa)

Cat’s claw has anti-inflammatory, antibacterial, antiviral, immune-modulating, and antioxidant properties. It contains quinovic acid glycosides, which are natural precursors to quinolones, a class of pharmaceutical antibiotics. It has been used as a stand-alone therapy and in conjunction with other antimicrobials (6).

Andrographis (Andrographis paniculata)

Andrographis is one of the best anti-spirochetal herbs for borrelial infections. This herb enhances immune function, protects the heart muscle, is anti-inflammatory, and crosses the blood-brain barrier. It is a systemic herb and helps correct inflammation-mediated neurodegeneration in the brain. It has been seen to prevent active infection when the tincture is applied topically and covered with bentonite clay for 24 hours to a bite site as soon as the tick is removed (12).

Japanese knotweed (Polygonum cuspidatum)

Red sage can normalize cytokine responses to microbial infections, in particular regulating unhealthy The most potent constituent in Japanese knotweed is resveratrol, a potent vasodilator, antiinflammatory, and inhibitor of platelet aggregation. Japanese knotweed modulates and enhances immune function, protects the body against endotoxin damage, and is highly protective of endothelial tissue. Japanese knotweed enhances blood flow and can cross the blood-brain barrier helping to reduce inflammation in the brain. It also helps other herbs and drugs enter difficult areas of the body to kill bacteria, making it a synergistic herb. It is a highly specific herb for Bartonella and Lyme infections (13).

Biocidin®LSF - Antimicrobial, Immunomodulatory, Anti-inflammatory Botanical Formulation

Biocidin®LSF has been a powerful tool in addressing Lyme disease in my patients, as it contains antimicrobial, anti-inflammatory, immune-modulating, and biofilm-breaking abilities. Additionally, its liposomal delivery is extremely helpful for enhancing intracellular absorption.

A year-long, in vitro study on the effect of Biocidin® Liquid and Biocidin®LSF liposomal formula on Borrelia, was completed with significant findings. The full, published article, which can be viewed here, looked at the Minimum Inhibitory Concentrations (MICs), Minimum Bacterial Death (MBD), and the time it took for these formulas to kill the Borrelia in vitro. Additionally, Dr. Leona Gilbert, one of the researchers who conducted the study, looked at all North American and European strains of Borrelia as well as the different pleomorphic forms (spirochete, blebs, round bodies, and biofilm) (14).

The MIC for the Liquid against all forms of the Lyme was 1:10, while the MIC for the LSF against all forms of the Lyme was 1:25. Using these dilutions, the formulas were exposed to 6 x 106 spirochetes in three ml of cultured media, and the cells were counted at 10, 20, 30, 60, and 120 minutes. In both scenarios, there was 97% cell death of the spirochetes in just 10 minutes after exposure to either Biocidin® delivery system. Even more impressive was the fact that the spirochetes did not morph into a cystic form, which will often happen when using potent antibiotic therapy.


Chronic Lyme disease is multifactorial, affecting every system of the body; thus, an integrative and systematic approach is the best way to successfully support recovery. Besides nutrient and botanical therapies that address the principles discussed in this article, lifestyle changes such as an antiinflammatory diet, addressing stress and hormone levels, and even managing PTSD should be focused on. Using a low-and-slow approach and implementing therapies strategically and simultaneously is the best way to achieve remission. There is no one protocol that will work for every person, so evaluating each individual’s presentation, labs, history, and symptoms will give the best insight into where to begin and how to build a successful treatment protocol.


  1. “Suggested Medication Protocols .” The Beginner’s Guide to Lyme Disease: Diagnosis and Treatment Made Simple, by Nicola McFadzean, BioMed Publishing Group, 2013, pp. 111-127.
  2. Burrascano, Joseph J. “Advanced Topics In Lyme Disease: Diagnostic Hints And Treatment Guidelines For Lyme And Other Tick-Borne Illnesses.” ILADS. Sixteenth Edition. 2008.
  3. “Treatment for Erythema Migrans.” Centers for Disease Control and Prevention, Centers for Disease Control and Prevention, 3 Nov. 2020,
  4. Peyriere, Hélène, et al. “Doxycycline in the Management of Sexually Transmitted Infections.” OUP Academic, Oxford University Press, 22 Nov. 2017,
  5. Daniel J Cameron, Lorraine B Johnson & Elizabeth L Maloney (2014) “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, 12:9, 1103-1135, DOI: 10.1586/14787210.2014.940900
  6. “Fundamentals of Natural Medicine in Lyme Disease .” The Beginner’s Guide to Lyme Disease: Diagnosis and Treatment Made Simple, by Nicola McFadzean, BioMed Publishing Group, 2013, pp. 139-178.
  7. Townsend, Danyelle M., Tew, Kenneth D., Tapiero, Haim. The importance of Glutathione in Human Disease. Biomedicine & Pharmacotherapy. Volume 57 issues 3-4 May 2003 Pg 145-155
  8. Chuan-li, L., Wei, Z., Min, W., Meng-mei, H., Wen-long, C., Xiao-jie, X., & Chuan-jian, L. (2015). Polysaccharides from Smilax glabra inhibit the pro-inflammatory mediators via ERK1/2and JNK pathways in LPS-induced RAW264.7 cells. Carbohydrate Polymers, 122, 428–436. doi:10.1 016/j.carbpol.2014.11.035
  9. “Initial Infection Dynamics, Cytokines, Encysted Forms and Biofilms .” Healing Lyme: Natural Healing of Lyme Borreliosis and the Coinfections Chlamydia and Spotted Fever Rickettsioses, by Stephen Harrod Buhner and Neil Nathan, 2nd ed., Raven Press, 2015, p. 114-165.
  10. Hucklenbroich, J., Klein, R., Neumaier, B., Graf, R., Fink, G., Schroeter, M., & Rueger, M. (2014). Aromatic-turmerone induces neural stem cell proliferation in vitro and in vivo. Stem Cell Research & Therapy, 5(4), 100. doi:10.1186/scrt500
  11. “Natural Healing of Chlamydia .” Healing Lyme: Natural Healing of Lyme Borreliosis and the Coinfections Chlamydia and Spotted Fever Rickettsioses, by Stephen Harrod Buhner and Neil Nathan, 2nd ed., Raven Press, 2015, p. 268-281.
  12. “The Materia Medica .” Healing Lyme: Natural Healing of Lyme Borreliosis and the Coinfections Chlamydia and Spotted Fever Rickettsioses, by Stephen Harrod Buhner and Neil Nathan, 2nd ed., Raven Press, 2015, p. 333-424.
  13. “Chlamydia .” Healing Lyme: Natural Healing of Lyme Borreliosis and the Coinfections Chlamydia and Spotted Fever Rickettsioses, by Stephen Harrod Buhner and Neil Nathan, 2nded., Raven Press, 2015, p. 240-255.
  14. Karvonen, Kati, and Leona Gilbert. “Effective Killing of Borrelia Burgdorferi in Vitro with Novel Herbal Compounds.” General Medicine Open, vol. 2, no. 6, 2018, doi:10.15761/gmo.1000153.