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Lyme Disease

Lyme disease is a confusing, potentially chronic and debilitating disease.  It is also a political mine field.  The politics of Lyme are so intense that it’s often impossible to understand the science of the situation.


I’m assuming if you are reading this, there is a good chance you have Lyme, or someone you love does.  Even if you are too brain fogged to get through this article, break it up and read it anyway.  This is important.

Lyme disease is a confusing, potentially chronic and debilitating disease.

In my opinion, an acute Lyme infection is Borreliosis.

Lyme disease is the combination of Borreliosis, plus other infections, PLUS YOU

What I mean by “you” is your metabolic health, methylation and detox capability, hormone status, stress level, genetic makeup, nutrition status and so much more.


Lyme Disease (LD) or Lyme Disease Complex is associated with the offending bacteria Borrelia burgdorferi (Borrelia).  There is also the potential of other concurrent infections called “co-infections.”  Infections are usually cleared by our immune system or with medical treatment.  Borrelia may alter your immune system so Borrelia and other infections together can’t be effectively cleared.  Lyme Disease Complex may also include other immune and metabolic problems.


There can be permanent damage from the bacteria. The persistence of Borrelia after “treatment” is a debatable point.  Persistence of an active Borrelia has been shown in different animal and human studies and it can cause permanent damage.


Two Standards of Care

One of the difficulties with respect to treatment is that there are two standards of care.  There is plenty of information regarding chronic Lyme disease available for public access.  Often the same documents are interpreted differently leading to support for either side of the standards of care.


The Center for Disease Control (CDC) and Infectious Disease Society of America (IDSA) recommend a two tiered testing approach followed by a course of antibiotic duration typically 14-28 days.  After the treatment, it is assured the Borrelia infection is dead and resolved, regardless of the patient.  For some people, the IDSA guideline is enough of a treatment for a complete and symptom free recovery.


The IDSA also recommends a single dose of Doxycycline 200 mg after a deer tick bite for the prevention LD.  The study this treatment is based on was designed to evaluate if this dose of Doxycycline stops the “bulls eye rash.”  The study wasn’t designed to determine if the person became infected with Borrelia after the single dose of antibiotics!  The study authors specifically pointed out that they were trying to determine the effect of antibiotics on the rash and not disease prevention.  People in the study had to drop out and get treated for Lyme!  The single dose did work sometimes.  There are good arguments that this “preventative” dose of antibiotics may be lead to difficult to diagnose chronic lyme infections by altering immune response and causing the bacteria to form persister cells.

Click to download one dose once study, (highlight on study mine.)


I highly recommend people understand the IDSA guidelines in detail, regardless of which treatment protocol you choose.  This is because medical practitioners follow the IDSA guidelines.  If you find yourself in that system, I encourage you to understand the approach.  I think rigid adherence to the guidelines is causing chronic Lyme disease in some people!

Download IDSA guidelines


Other practitioners suggest a much longer antibiotic approach, which may include “alternative” therapies.  This group includes the International Lyme and Associated Diseases Society (ILADS), of which I’m a member.  ILADS guidelines simply suggest why the IDSA criteria isn't sufficient in some cases, using research to demonstrate those points. ILADS guidelines are not a treatment protocol. 

Download ILADS guidelines


Unfortunately, there are some people who don’t have complete recovery from the IDSA “short” course of antibiotics.  There may be many reasons for this treatment failure.  The problem is a combination of Borrelia’s ability to evade the antibiotic and an individuals metabolic and immunologic health.


Some people also have other problems triggered by Borrelia that go beyond the persistence of a Borrelia infection. Meaning some people do have “post Lyme infectious syndrome”, as suggested by the IDSA.


This can include:

  • Autoimmune diseases that were triggered

  • Metabolic damage like mitochondrial energy production problems

  • Gut infections triggered caused by the antibiotics.


Borrelia has a lot of defense mechanisms:

Borrelia has a lot more DNA than most infections we get.  This means that Borrelia has more capability to be aggressive, avoid your immune system and overcome treatment.

Borrelia is hard to kill with antibiotics:

  • The bacteria has a slow life-cycle

    • Antibiotics are most effective during replication so a slow life-cycle requires a longer treatment

  • Borrelia has the ability to hide inside you

    • It can hide in places your immune system and antibiotics can’t reach

      • Tendons, spaces within cells, nerves and brain cells

  • Borrelia can form persister cells

    • It stops growing entirely and persists until the antibiotics are gone

  • Borrelia can change its shape and membrane structure (morphology)

    • Helping it become resistant to otherwise lethal doses of antibiotics without the need of gaining antibiotic resistance through genetic changes. (click to download an example study)


If the antibiotics were enough to completely kill the infection and no further diseases were triggered by the bacteria, you should be symptom free...especially by the end of the treatment.


The misconception of antibiotics is that they are able to completely eradicate an infection.


The IDSA criteria for an antibiotic treatments may not be a strong enough or long enough dose for Lyme disease.  Antibiotics may kill or stun a large percentage of bacteria during an infection.  We then assume your immune system will remove the remaining bacteria. People with cancer, autoimmune diseases, elderly, infants and the immune suppressed are more susceptible to infections without recovery because of decreased immune response.  It is possible the combination of your immune system and antibiotic efficacy is not enough to clear Borrelia from your system, especially because Lyme can change your immune system.  Often people with decreased immune responses are treated more aggressively for other infections, why not Lyme?


Borrelia can evade your immune system by altering it.  Your immune system has a choice in the way it can fight infections.  You can fight infections via immune cells attacking the infection directly (cell mediated immunity) or you can make proteins that stick specifically to that infection (antibody mediated immunity).  The balance between antibody and cell mediated immunity is critical. Ideally our immune system should attack Borrelia with an large antibody response and a proper cell mediated immune response.


Borrelia can alter your immune system


Borrelia has the ability to alter both antibody and cell mediated immune functions.  Inflammation is the conversation of your immune system.  Inflammation is a chemical mix your immune system makes to be able to converse with itself and other cells.  Borrelia can causes changes in production of those chemicals, thereby changing your immune system's function.  Borrelia can use your immune system's conversation to protect itself.



Lyme likes and causes inflammation


  • It can cause a decrease in antibody production

  • It can change the way you switch from IgM to IgG antibody making chronic infections look acute

  • It can alter cell medicated immunity

  • I can alter the chemical conversation of inflammation





I feel it’s necessary to know if you have Borrelia.  Don’t assume Lyme!  Don’t treat all joint and muscle pain with fatigue as Lyme.


Testing for Lyme disease is controversial and potentially inaccurate.  Many Lyme disease cases are missed with standard testing.  There is also no follow-up test to determine if the treatment has been effective.  I use multiple different types of tests to try to overcome this.


IDSA's two tier testing dictates first do an ELISA and then confirm with a Western blot.

Both the ELISA and WESTERN BLOT are antibody detection tests.  The ELISA is a generalized “do you have antibodies to Borrelia?”  The western blot follow up is “do you have antibodies to this part of Borrelia? How about this part of Borrelia?”


Positive testing requires a strong antibody response.


Borrelia has the ability to reduce antibody production, which can make the IDSA criteria testing NEGATIVE.  A negative result may mean no exposure to Borrelia, exposure to a different strain than the one tested for or exposure with insufficient antibody response.


I frequently suggest antibody testing such as the standard western blot or more sensitive testing such as Igenex testing, which may include a western blot or the new improved Lyme ImmunoBlot.  Please keep in mind no testing is 100% accurate, so finding bits of information on various tests can be helpful.

You can get more information about Igenex Testing here.

 You can also test blood for a cell mediated immune response.  Several companies offer this test.  Cell mediated immunity can indicate exposure to Borrelia much sooner than antibodies, because antibody production takes more time for your immune system.  People who have altered immune reaction may only have a measurable cell mediated immune response.

Download information about Igenex Lyme IGX spot cell mediated immunity test.


Igenex Website link to the IGX Spot


You can look for the Borrelia organism as well.  Why test for your immune system when you can just find the infection itself?  There are multiple types of Borrelia cultures and antigen tests available (antigens are pieces of Borrelia, so in essence, you look for pieces of the bacteria in some way).


If you have an infection such as a urinary tract infection, meningitis or strep throat the practitioner would look for the infectious organism, not just immune system’s response. Yet with Borrelia, the IDSA insists on only asking our immune system… which may duped by the infection.


There are multiple ways to detect the Borrelia directly.  Some methods are more accurate than others.  I prefer an antibiotic challenged urine antigen and PCR test through IgeneX but there are multiple choices out there, including cultures.


Why don’t practitioners use these other tests?  Why not culture or antigen testing?  Well here is the IDSA guideline quote about that:


Although useful for documentation of B. burgdorferi infection in research studies, amplification of B. burgdorferi DNA by PCR or culture of specimens of skin or blood for Borrelia species is not recommended for diagnosis of erythema migrans in routine clinical care because of the cumbersome nature and expense of these test methods.


Cumbersome and expensive, that’s it?!?  That’s the reason the IDSA states.  If those tests are used and come out positive, ISDA members generally disregard the results and insist on an ELISA and then Western Blot.


You want to know what I think is cumbersome and expensive?  Having Lyme disease undetectable by IDSA criteria.  Traveling to a string of IDSA doctors who tell you you are crazy, depressed, emotional, faking it and making up a disorder.  That’s cumbersome… and expensive.   I digress.


If you are a doctor, you want an answer yesterday.  I sure do.  I love labs! A person may take 4-6 weeks after exposure to make antibody to Borrelia.  It may take three to six weeks to get test results on a culture or antigen detection.  Cell mediated immunity testing is accurate earlier, but not easily available to ISDA doctors.  This can be bulky and cumbersome for general screening, but that doesn’t make these tests invalid.


I use the Igenex urine antigen PCR panel test frequently because the test finds Borrelia pieces in your urine during an antibiotic challenge.  This test is not accepted by IDSA criteria.  The test can find either DNA or protein from Borrelia in your urine.  It is most accurate during the first several days of an antibiotic treatment, especially in a long standing Borrelia infection.  My take is, if you pee out Borrelia pieces, you likely have the Borrelia in you.


If you had the classic “bulls eye rash” (erythema chronicum migrans), you can be certain you have to Borrelia, but only 50% of people at most get the rash.  Don't forget 200mg doxy one dose once prevents the rash.  Other indicators of a Borrelia infection may include migrating muscle and joint pains, heart problems and neurological symptoms.


Lyme symptoms may include:

Acute Symptoms: Flu like illness, Fever, chills, sweats, muscles aches, fatigue, nausea and joint pain.


Chronic symptoms: fatigue, low grade fevers, night sweats, sore throat, swollen glands, stiff neck, migrating joint pain, stiffness, arthritis, muscle pain, chest pain, palpitations, abdominal pain, nausea, diarrhea, sleep disturbances, poor concentration and memory loss, irritability and mood swings, depression, back pain, blurred vision and eye pain, jaw pain, testicular/pelvic pain, tinnitus, vertigo, headaches, light-headed, dizziness and cranial nerve disturbances (facial pain, tingling, Bell's palsy or ear and eye damage)


Lyme Disease Treatments


I use natural treatments for most conditions, but I feel antibiotics are an integral part of successful Lyme disease treatment.  Antibiotics are especially useful in acute borreliosis which tends to have a full resolution.  I do not believe antibiotics are enough for everyone.  I also suggest herbal anti-microbials and other treatments to support the “you” part of the equation.


Ineffective short courses of antibiotics, or other treatments like cortisone, prednisone or anti-inflammatory steroids, often drive Borrelia into defensive positions and can cause severe and unchangeable chronic disease.


A common issue in treating Lyme is the Herx reaction.  Herx reactions are not specifically what symptoms are present, it’s that the symptoms come and go.  This is due to the organisms dying and your immune response. Expect Herx reactions when treating Lyme disease with antibiotics and/or natural treatments.  The Herx reaction guides the treatment and also helps to confirm Lyme, especially during therapeutic treatment trials.  People who have Herx reactions and feel better faster, tend to stay well.  One way to know your treatment is done, is that the herx reactions are gone.  This can take a long time in chronic cases.


Herx reactions are one of the indications that you do have an Borrelia infection.  Monitoring and tracking your herx reactions is essential for proper treatment.  If you are still having herx reactions, you still have an active infection.  That is a reason to continue treatment.  If you are following IDSA protocol and still have symptoms near the end of the treatment, it is advised to find someone that is willing to continue the treatment past your herx reactions.  At this point, I change treatments and include prescriptions that can kill the persister cells.


Steroids can make LD worse and chronic.  The goal of a prednisone treatment is to suppress your immune system.  Doctors may treat Lyme symptoms with prednisone or steroids because the IDSA testing for LD was negative.  Sadly, the emergency nature of some Borrelia symptoms require steroid treatment.  Suppressing your immune system with steroids helps the Borrelia hide and change your immune system further.  If I suspect symptoms are LD related, I suggest using antibiotics as well.


Integrative Lyme Disease Treatment

I consider antibiotic use for Lyme necessary, but I also think there is MORE that needs to be done at the same time, to make sure the treatment is successful.  This is especially true if you’ve been unsuccessfully treated or are living with chronic Lyme disease.



A comprehensive Borrelia treatment should consider:

  • Antibiotics appropriate to the disease state and co-infections

  • Herbs that may also kill Borrelia and co-infections (examples not all inclusive)

    • Bacteria: Teasel, Guiacum, cat's claw, Houttuynia, grapefruit Seed extract, Buhner's suggestions, Zhang formulas, Byron white formulas, etc

    • Viruses: scutellaria baicalensis, Olive, Cedar, Lemon Balm, elderflower

    • Parasites: Sida, Alcornea, Cryptolepsis, Copmine

    • Fungus: Grapefruit seed extract, Caprylic acid, Essential oils

  • Glutamine to help protect your gut lining from damage

    • The amino acid L-glutamine is the main food your gut lining can eats and can help reduce antibiotic associated gut aggravation

  • Probiotics

    • To help protect the organisms in your gut from the antibiotics

  • Immune modulators

    • Especially favoring antibody production

  • A biofilm treatment

    • Herbal and/or enzymes

  • Supportive treatments:

    • Adrenal, thyroid, heavy metal chelation, liver detox, methylation, antioxidants, mitochondrial, etc

  • Appropriate diagnosis and lab monitoring

    • Through the entire process to reduce risk and side effects as much as possible



Borrelia May Be Persistent


Another argument between IDSA and ILADS is if the consequences of a Borrelia infection are from “post lyme related consequences” or a persistent active Borrelia infection.  I think the answer is both.  It is on the practitioner to figure out if the infection is still active or if the symptoms present are repercussions of resolved LD.  There are many studies that show Borrelia can be persistent after aggressive treatments in dogs, mice, monkeys and humans.


The first goal of treating Borrelia is to kill the infection, but that may not be possible.  The second goal of treating Borrelia is to get the infection as managed as possible.  Sometimes Lyme is about management.  In my treatments, I always intend to kill the infection first with well planned individualized comprehensive integrative treatments.  I think that borreliosis (acute lyme) is killable and chronic lyme may not be.  You may find yourself at a point that you have to manage the infection and keep the symptoms at a minimum.  What management means is specific to each person.  Often effective management is keeping inflammation down through diet, lifestyle and treatments. Sometimes management means taking antimicrobials to keep the Borrelia suppressed.


The goal remains the same: Pain free, healthy, happy, functional life.


I feel integrative doctors, like Naturopaths, are uniquely suited to treat parts of the entire Lyme disease complex that may be missed with antibiotic only treatments.  A practitioner covered by your insurance may be necessary for testing and prescriptions.  Therefore a team of integrative doctors is ideal for certain difficult chronic cases, if not all cases.


I suggest engaging an ILADS “Lyme literate doctor” to help you with this complicated treatment. Referrals for “lyme literate” physicians may be obtained through

Provider search on


In Summary, I think Lyme is a combination of Borrelia, plus other infections, plus you.  A comprehensive, well tested and planned treatment is ideal for killing or managing Lyme disease.  Borrelia gives us a lot of opportunities to learn about ourselves, health care and the science of infections.  I'm hoping we can overcome political feuds and medical misunderstanding and help Lyme disease suffers live their optimal life.


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