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Lyme disease, MSIDS and Natural Lyme Treatments
What are Lyme disease and MSIDS?

The short version of an answer: Lyme disease is an infection caused by the spirochete bacteria Borrelia burgdorferi, at times causing a 'bulls-eye' rash, which may not diagnosed or treated in a timely fashion, perhaps due to multiple factors including a highly varied patient presentation and many doctors' erroneous dependence on problematic testing.  In such scenarios, the spirochetes may propagate, becoming more deeply embedded and difficult to treat, and a person may end up with long-term problems and a chronic infection.

But if you, the reader, came here for more, well then, you came to the right place!

Lyme disease, or 'lyme borreliosis', is one of multiple infections which can be transmitted by ticks, many of which by themselves or collectively together as 'co-infections', can result in a staggering and far-reaching set of chronic symptoms, called 'Multiple Systemic Infectious Disease Syndrome' (MSIDS).  Lyme disease and the bacteria that cause it are the most famous, or rather infamous, among babesiosis, bartonellosis, anaplasmosis, ehrliciosis, Powassan virus, Tick Borne Relapsing Fever, and other tick-borne illnesses thus it will be the focus here.

Year after year, Lyme disease continues to be rapidly spreading across the entire world, not just the United States.   A study published in 2022 found more than 14 percent of the world's population has had Lyme disease, with the highest rates in Central Europe, Eastern Asia, Western Europe, and Eastern Europe respectively. (1)  While closer to home here in the US, from 2007 to 2021, private insurance claim lines with Lyme disease diagnoses rose 357 % in rural areas and 65 percent in urban areas. (2)  Other alarming statistics exhibiting the rapidly spreading incidence of Lyme disease include that there has been a 320% increase in the number of US counties affected with Lyme disease within the past 20 years (3), as well as that the number of reported cases of disease from mosquito, tick, and flea bites (collectively referred to as 'vector-borne illnesses') have more than tripled from 2004 to 2016. (4)  Among the almost 650,000 vector-borne reported cases during this 12-year period, over 491,000 were tick-borne. (5) 


Some recently popularized statistics contrast cases that are reported against what actually gets diagnosed.  Each year, approximately 35,000 cases of Lyme disease are reported to Center for Disease Control and Prevention (CDC) by state health departments but this number does not reflect every case of Lyme disease that is diagnosed in the United States every year. Standard national surveillance is only one way that public health officials can track where a disease is occurring and with what frequency.  And since not all diagnosed cases get reported, recent estimates using slightly older insurance claims data suggest that approximately 476,000 people may get Lyme disease each year in the United States. (6)


natural treatment for Lyme disease

But to understand how Lyme disease has become so rampant, one must comprehend that the organism responsible for Lyme disease is not just one 'superbug'; it is many!  

Lyme disease is not as simple as just being one organism-one disease!  Lyme disease is caused by several species and subspecies of spiral-shaped bacteria – or 'spirochetes' – from the group Borrelia, many of which are constantly evolving, highly advanced, and great at outflanking mammalian host immune system resolution.  The bacteria identified in the northeastern USA as the causative agent for 'Lyme disease', associated with Lyme, Connecticut, is Borrelia burgdorferi.  But did you know there are different strains of Borrelia burgdorferi? "Immunological and genetic techniques used to elucidate genetic, phenotypic, and immunological heterogeneity in B burgdorferi have demonstrated a considerable degree of genetic variation, [with] more than 100 different strains from the United States and at least 300 worldwide are listed." (7)  The two most pathogenic and extensively studied, namely B. burgdorferi B31 and 297 are not even both used by many commercial laboratories.  Many ELISA and Western blot Lyme disease tests are only equipped to detect one strain of one species of Borrelia: Borrelia burgdorferi B31 (Bb ss B31). This means that those tests may be missing infections caused by other strains and/or species of Lyme borrelia. (8)  With most labs use of only B31 for their testing, this creates one level of diagnostic issues, problems, and false negatives.  These two strains are collectively known as 'Borrelia burgdorferi sensu stricto' and are transmitted by the black-legged deer tick. B. burgdorferi s. s. is the predominant species in North America but is also common in Europe.  And yes, people have been shown to be infected with more than one strain at a time. (7).

Black legged deer tick

But beyond different strains within a single species, there are other species of Borrelia as well, several of which have been shown to cause the infection known as Lyme disease'Borrelia burgdorferi sensu lato 'complex includes 20 named spirochetes, mostly with limited distribution, "...and a still not named group proposed as genomospecies. Descriptions of new species and variants continue to be recognized, so the current number of described species is probably not    

naturopathic doctor near me

B.burgdorferi s.s. spirochetes.  Courtesy of CDC

final." (9,10)   Of the ten species with pathogenic potential, the three most commonly associated with infections in humans are the before mentioned B. burgdorferi s.s., B. afzelii, and B. garinii.  Others include B. bavariensis (which itself used to be included in B. garinii), B. bissettii, B. kurtenbachii, B. lusitaniae, B. spielmanii, B. mayonii, and B. valaisiana.  Furthermore, since,  to our knowledge, none of the local labs test for any of these Borrelia species beyond B. burgdorferi B31, this becomes another way in which people are not accurately diagnosed with having a current Lyme disease infection.

MSIDS is a term used to describe a “symptom complex” that can create persistent and tenacious illness. It was coined by Dr. Richard Horowitz, M.D., a board-certified internist, renowned Lyme disease specialist, author, and researcher.  "MSIDS is a
multifactorial model for treating chronic disease(s), which identifies up to 16 overlapping sources of inflammation and their downstream effects."
  This paradigm shift away from 'one infection-one antibiotic' shares a fundamental approach with the tenants of naturopathic medicine including 'Identify and Treat the Causes' and 'Treat the Whole Person'.  

Factors on the 16-point MSIDS model, which are then evaluated based on the patient's history and physical examination, and can contribute to chronic illness include:

  • Lyme disease and co-infections

  • Immune dysfunction

  • Inflammation

  • Environmental toxins

  • Nutritional deficiencies

  • Mitochondrial dysfunction

  • Endocrine abnormalities

  • Neurodegenerative disorders

  • Neuropsychiatric disorders

  • Sleep disorders

  • Autonomic nervous system dysfunction and POTS

  • Allergies

  • Gastrointestinal disorders

  • Liver dysfunction

  • Pain disorders/addiction

  • Lack of exercise/deconditioning

Why use integrative medicine to treat Lyme disease?

"One of the most important understandings now facing us is accepting the limits of pharmaceuticals in the treatment of many of these emerging diseases.  While antibiotics do still have a role, sometimes a very important one, they can no longer be relied on to provide the sole response to these kind of infections as they spread through the human population." (12)

In the face of increasing incidence of antibiotic resistance among multiple types of

bacteria, as well as our increased understanding of how different bacteria will exchange segments of DNA, thereby sharing resistance and virulence information, there has been multiple publications on what have come to called 'persisters'. (13,14)  "Persisters are elusive, present in low numbers, ... multi-drug-tolerant cells that can change with the environment. ... Persisters can adopt varying sizes and shapes, changing from well-known forms to altered morphologies. ... Persisters remain viable despite aggressive antibiotic challenge and are able to reversibly convert into motile forms in a favorable growth environment." (13)

natural treatment for Lyme disease

 **image credits

Beyond the possible limitations of some antibiotic therapies, conventional care also almost invariably has very limited knowledge about, or management options for, jarisch- herxheimer reactions (JHR)"JHR is a transient clinical phenomenon that occurs in patients infected by spirochetes who undergo ... treatment. More specifically, the reaction occurs within 24 hours of antibiotic therapy for spirochetal infections, including syphilis, leptospirosis, Lyme disease, and relapsing fever. It usually manifests as fever, chills, rigors, nausea and vomiting, headache, tachycardia, hypotension, hyperventilation, flushing, myalgia, and exacerbation of skin lesions." (15) These responses to treatment have long been recognized in the literature when antibiotics are given to patients with syphilis, (16) yet if the symptoms are even acknowledged by conventional doctors, they often do not direct patients to incorporate the detoxification and lymphatic drainage support needed for relief.  Naturopathic physicians have significant training in these areas.

Why use integrative medicine to treat

Unfortunately with so many conventional medical doctors having compromised whole-person care for symptom management, abbreviated office visits and continual referral to different specialists, there has been a shortage of medical professionals with a 'big picture' approach.  

MSIDS requires exactly this 'big picture' approach!  "This may be the reason why so many people don't improve with standard Lyme treatments, such as one month of doxycycline or Rocephin.  The design of many ... studies on the best treatments for Lyme disease do not take into account these potential multifactorial causes, so giving only one or two antibiotics for a short period of time only addresses a small piece of the complex puzzle.  The answers lie in a more holistic diagnostic approach."(8)

functional medicine doctor near me

For over a century, naturopathic physicians have sought to treat patients by restoring balance and proper function in the least invasive way possible.  One of the principles of this medicine, Vis Medicatrix Naturae, which translates to 'The healing power of nature' advances that "[i]t is the naturopathic physician’s role to support, facilitate and augment this process by identifying and removing obstacles to health and recovery, and by supporting the creation of a healthy internal and external environment." (17)

Naturopathic physicians that are board certified and practicing in licensed states have received four years of rigorous training and passed multiple licensing exams.  This allows for a therapeutic approach that does more than just manage symptoms with pills and five to ten minute follow-ups.  Rather, individualized testing and lifestyle considerations, used in conjunction with revitalizing energetic and/or physical medicine therapies are major tenants to a successful program which seeks to enable a person's recovery and succeed where others have not.

Support for patients with Lyme disease

Evidenced-based herbal medicine

Multiple medicinal herbs have been shown in the literature to be helpful in killing the bacteria which cause Lyme disease (18, 19, 20) and many botanicals have been used for centuries to support the body's systems that are addressed in MSIDS.  Though several famous herbal protocols have been in use for years including Buhner, Cowden, and Zhang and helped many patients, the research has been catching up with documenting use of some of these antimicrobials against different forms of Borrelia.  For though there are different species and subspecies of Lyme disease, one given species can alter its morphology, making it resistant to certain types of treatment.  "Persisters can adopt varying sizes and shapes, changing from well-known forms to altered morphologies. They are capable of forming round bodies, L-form bacteria, microcolonies or biofilms-like aggregates, which remarkably change the response of Borrelia to hostile environments." (13)This goes a long way to the staying power of Lyme disease in the host, and why different protocols may be required at different times.


Advanced specialty testing

The commercially available present Lyme disease two-tiered testing strategy was really intended for surveillance purposes and, though it has a high specificity averaging around 99%, it is known to have a horrifically low sensitivity averaging around 56%. (21)   Furthermore, per the CDC, the surveillance case definitions are not intended to be used by healthcare providers for making a clinical diagnosis or determining how to meet an individual patient’s health needs", (22) though this is repeatedly what happens in practice.  And scores of patients are denied treatment because their two-tier testing was negative, despite having clinical symptoms.   In this state of affairs, approximately half of the individuals with Lyme disease may go undiagnosed.  Because of these issues and similar concerns when testing for co-infections, our clinic will often use specialty labs which have more comprehensive and reliable testing options.  

Effective use of vitamins, minerals and nutritional supplements

The entire premise of MSIDS is an acknowledgement that treating a patient requires more than just considering whatever diagnostic label this person has been given.  Attempting to restore balance to our bodies in the least invasive manner possible is part of the philosophic approach of naturopathic physicians.  Thus we often seek to use the body's constituents to see if better health can be achieved, especially in light of findings from advanced nutritional testing.  These may include vitamins, minerals, amino acids, fatty acids, supplemental hormones and more as we try to support multiple organ systems and homeostatic mechanisms.  And interestingly, some nutritional supplements, not just herbs, have been shown to be effective in the literature against particular mechanisms like biofilms, which are employed by many types of bacteria, including the spirochetes of Lyme disease. (23)

Don't get stuck not trying acupuncture

Research hot of the press and published in 2022 using mice infected with Lyme disease and treated with electroacupuncture found the "... electro-acupuncture induced a lasting anti-inflammatory effect on mice. Despite the discontinuation of treatment at 2 weeks, the simultaneous decrease in neutrophils in the joints and inflammatory cytokine levels throughout the body at 4 weeks suggests a systemic and persistent effect of electroacupuncture that attenuates Lyme arthritis. Our results suggest that electroacupuncture-mediated anti-inflammatory responses could offer promising healthcare benefits in patients suffering from long-term Lyme disease manifestations." (24)  But beyond just attenuating the immune system when faced with an infection, acupuncture has been shown to be effective treatment for many concerns that fall beneath the MSIDS considerations, including inflammation, allergies, neuropsychological issues, autonomic nervous system dysfunction, endocrine abnormalities, gastrointestinal disorders, pain management and more.  Specifically, the World Health Organization (WHO) issued a report back in 2002-2003 and concluded a review of over 200 clinical trials and deemed acupuncture as effective for 28 diseases and beneficial for 63 others! (25)

Removing barriers to wellness: Exploring endocrine disruptors, environmental contaminants, and how we detoxify them

While many chemicals, both natural and man-made, may mimic or interfere with our hormones, some have become so common in our day to day lives, that they have warranted special investigation and review.  Called "endocrine disruptors", these chemicals are linked with developmental, metabolic, reproductive, brain, immune, and other problems in different organs and glands of the endocrine system, which is the hormone-based communication network in the body. Endocrine disruptors include bisphenol A, dioxins, perchlorate, perfluoroalkyl and polyfluoroalkyl substances (PFAS), phthalates, phytoestrogens, polybrominated diphenyl ethers (PBDEs), polychlorinated biphenyls (PCBs), and triclosan, among others.

Heavy metals are another group of environmental contaminants that have found their way into many people living in the modern world.  This added toxicity burden impairs the immune system enough to make it harder for dealing with any infection.  As shown in a study from 2007 which compared mice infected with Borrelia burgdorferi with similarly infected mice but ones also laden with mercury, "[infected and mercury laden] mice showed less ...  delayed eradication of spirochetes compared to mice, [that were only infected]". (26)

Some people won't improve until their previous body burdens and impediments to optimal health have been removed.  These can be in the form of heavy metals, nutritional or enzyme deficiencies, mitochondrial dysfunction, endocrine abnormalities or psychological stressors; naturopathic physicians are specifically trained to deal with these issues. 

Therapeutic lifestyle medicine

Taking prescription medicines, nutritional supplements or other aides while living a lifestyle that impedes progress ultimately sets a patient up for lukewarm success.  The benefits of anti-inflammatory diets, exercise, and meditation have been expounded in the literature, for dietary triggers could "... exacerbate symptoms for those with Lyme-MSIDS, who already have ongoing inflammatory responses caused by the same cytokines." (8)  

So if you are seeking guidance, support or treatment, consider contacting our clinic at the number above.











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1. Dong, Yan et al. “Global seroprevalence and sociodemographic characteristics of Borrelia burgdorferi sensu lato in human populations: a systematic review and meta-analysis.” BMJ global health vol. 7,6 (2022): e007744. doi:10.1136/bmjgh-2021-007744.

2. Fair Health. Lyme Disease Diagnoses Increased 357 Percent in Rural Areas over Past 15 Years, according to Private Insurance Claims. Accessed 11-15-22.

3. Kugeler, K.J.; Farley, G.M.; Forrester, J.D.; Mead, P.S. Geographic Distribution and Expansion of Human Lyme Disease, United States. Emerg. Infect. Dis. 2015, 21, 1455–1457. 

4. Center for Disease Control and Prevention. Vital Signs.  Illnesses on the Rise.  Accessed 11-15-22.

5. Rosenberg, R. Vital Signs: Trends in Reported Vectorborne Disease Cases—United States and Territories, 2004–2016. MMWR Morb. Mortal. Wkly. Rep. 2018, 67.

6. Center for Disease Control and Prevention. Data and Surveillance.  How Many People Get Lyme Disease? .  Accessed 11-15-22.


7. Seinost, G et al. “Infection with multiple strains of Borrelia burgdorferi sensu stricto in patients with Lyme disease.” Archives of dermatology vol. 135,11 (1999): 1329-33. doi:10.1001/archderm.135.11.1329. 

8. Horowitz, R. Why Can’t I Get Better? Solving the Mystery of Lyme and Chronic Disease, 1st ed.; St. Martin’s Press: New York, NY, USA, 2013; ISBN 978-1-250-01940-0. Pg 58, 63, 373.

9. Rudenko, Nataliia et al. “Updates on Borrelia burgdorferi sensu lato complex with respect to public health.” Ticks and tick-borne diseases vol. 2,3 (2011): 123-8. doi:10.1016/j.ttbdis.2011.04.002.

10. Margos, Gabriele et al. “Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov. prevail in diverse enzootic transmission cycles.” International journal of systematic and evolutionary microbiology vol. 66,3 (2016): 1447-1452. doi:10.1099/ijsem.0.000897.

11. Horowitz, Richard I, and Phyllis R Freeman. “Precision Medicine: The Role of the MSIDS Model in Defining, Diagnosing, and Treating Chronic Lyme Disease/Post Treatment Lyme Disease Syndrome and Other Chronic Illness: Part 2.” Healthcare (Basel, Switzerland) vol. 6,4 129. 5 Nov. 2018, doi:10.3390/healthcare6040129.

12. Buhner, S. Natural Treatments for Lyme Coinfections: Anaplasma, Babesia, and Ehrlicia, 1st ed.; Healing Arts Press: Rochester, VT, USA, 2015; ISBN 978-1-62055-258-2. Pg 16.

13. Rudenko, Natalie et al. “Metamorphoses of Lyme disease spirochetes: phenomenon of Borrelia persisters.” Parasites & vectors vol. 12,1 237. 16 May. 2019, doi:10.1186/s13071-019-3495-7. 

14. Feng, Jie et al. “A Drug Combination Screen Identifies Drugs Active against Amoxicillin-Induced Round Bodies of In Vitro Borrelia burgdorferi Persisters from an FDA Drug Library.” Frontiers in microbiology vol. 7 743. 23 May. 2016, doi:10.3389/fmicb.2016.00743.

15. Dhakal, Aayush. and Evelyn Sbar. “Jarisch Herxheimer Reaction.” StatPearls, StatPearls Publishing, 28 April 2022.


16. “Jarisch-Herxheimer reaction.” British medical journal vol. 1,5537 (1967): 384.

17. Snider, Pamela, and Jared Zeff. “Unifying Principles of Naturopathic Medicine Origins and Definitions.” Integrative medicine (Encinitas, Calif.) vol. 18,4 (2019): 36-39.


18. Feng, Jie et al. “Evaluation of Natural and Botanical Medicines for Activity Against Growing and Non-growing Forms of B. burgdorferi.” Frontiers in medicine vol. 7 6. 21 Feb. 2020, doi:10.3389/fmed.2020.00006.

19. Brorson, O, and S-H Brorson. “Grapefruit seed extract is a powerful in vitro agent against motile and cystic forms of Borrelia burgdorferi sensu lato.” Infection vol. 35,3 (2007): 206-8. doi:10.1007/s15010-007-6105-0. 

20. Datar, A. et al. "In Vitro Effectiveness of Samento and Banderol Herbal Extracts on the Different Morphological Forms of Borrelia Burgdorferi." Townsend Letter, the Examiner of Alternative Medicine. 2010-07.

21. Stricker, Raphael B, and Lorraine Johnson. “Lyme wars: let's tackle the testing.” BMJ (Clinical research ed.) vol. 335,7628 (2007): 1008. doi:10.1136/bmj.39394.676227.BE

22. Center for Disease Control and Prevention.  National Notifiable Diseases Surveillance System (NNDSS).  Case Definitions.  Lyme disease (Borrelia burgdorferi)
2022 Case Definition. Accessed 11-20-22.

23. Dinicola, S et al. “N-acetylcysteine as powerful molecule to destroy bacterial biofilms. A systematic review.” European review for medical and pharmacological sciences vol. 18,19 (2014): 2942-8.

24. Akoolo, Lavoisier et al. “Sciatic-Vagal Nerve Stimulation by Electroacupuncture Alleviates Inflammatory Arthritis in Lyme Disease-Susceptible C3H Mice.” Frontiers in immunology vol. 13 930287. 18 Jul. 2022, doi:10.3389/fimmu.2022.930287.

25. World Health Organization. Acupuncture: Review and Analysis of Reports on Controlled Clinical Trials. Geneva: World Health Organization; 2003.

26. Ekerfelt, C et al. “Mercury exposure as a model for deviation of cytokine responses in experimental Lyme arthritis: HgCl2 treatment decreases T helper cell type 1-like responses and arthritis severity but delays eradication of Borrelia burgdorferi in C3H/HeN mice.” Clinical and experimental immunology vol. 150,1 (2007): 189-97. doi:10.1111/j.1365-2249.2007.03474.x.

27. **image credits. Center for Disease Control and Prevention.

The content and any recommendations in this article are for informational purposes only. They are not intended to replace the advice of the reader's own licensed healthcare professional or physician and are not intended to be taken as direct diagnostic or treatment directives. Any treatments described in this article may have known and unknown side effects and/or health hazards. Each reader is solely responsible for his or her own healthcare choices and decisions. The author advises the reader to discuss these ideas with a licensed naturopathic physician.


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