Lyme Disease

IDSA protocol
Ilads Criteria
How to test for Borrelia
Symptoms of Borellia and Co-infections
Goals of Treatment

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

Having an acute infection with Borrelia is Borreliosis.

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

(your metabolic health and your inflammation!)

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 it, break it up and read it anyway.  It’s important.


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 difficult or impossible to understand the science of the situation.


Lyme Disease (LD) or Lyme Disease Complex is associated with the offending bacteria Borrelia burgdorferi (Borrelia) or other Borrelia species.  There is also the potential of other concurrent infections called “co-infections.”  Organisms are usually cleared by our immune system or infectious disease treatment.  Borrelia may alter your immune system so that Borrelia and the other infections together can’t be effectively cleared.  Lyme Disease Complex may also include other inflammatory problems, autoimmune diseases and consequences of a dysregulated immune system and permanent damage from the bacteria.  The persistence of Borrelia after “treatment” is a debatable point.  Persistence of Borrelia has been shown in different animal and human studies.


There is plenty of information regarding chronic Lyme disease available for public access. One of the difficulties with respect to treatment is that there are two standards of care.
IDSA Protocol

IDSA Protocol
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 then assumed the Borrelia infection is dead and resolved.  In some people, the IDSA guideline is enough of a treatment for a complete symptom free recovery.

 IDSA arguments

There are many arguments regarding the IDSA guidelines.  In a statistical review in 2012 brought into question the accuracy of the analysis of the IDSA studies.  The entire criteria on which the IDSA guidelines are built on mistaken analysis of the studies performed to write it.  For instance the studies used to write the IDSA guidelines showed that longer treatments were effective and necessary but the statistics used to evaluate the study were done incorrectly showing the opposite result.   The IDSA also recommended a single dose of Doxycycline 200 mg after a deer tick bite a presumptive preventative treatment for Lyme Disease.  Sadly, the study this treatment is based on was designed to evaluate if this dose of Doxycycline stops bulls eye rash. The study wasn’t designed to determine if the person became infected with Borrelia after the single dose of antibiotics and discontinued monitoring patients after 6 weeks. 9, 12   

The explanation of why the study for single dose doxycycline only looked for the ECM rash to diagnose lyme (not other symptoms)…

“this end point was chosen deliberately. Erythema migrans at the site of the bite is the most common clinical manifestation associated with B. burgdorferi infection and is the only reliable marker of infection caused by that specific bite.”


There are good arguments that this preventative dose of antibiotics may be lead to difficult to diagnose chronic Borrelia infections!  Click to read more.


I highly recommend people understand the IDSA guidelines in detail, regardless of which treatment protocol you choose.  This is because most of the medical establishment follows the IDSA guidelines.  If you find yourself engaged with that system, you have to understand the approach as it will be aggressively adhered to.

Click here to download the IDSA guidelines if you haven’t already done so from above links.
Ilads Criteria

ILADS Criteria

Other practitioners use a much longer antibiotic approach, with or without alternative complementary treatments. This group includes the International Lyme and Associated Diseases Society (ILADS), of which I’m a member.  ILADS criteria varies from the IDSA guidelines in both diagnostics and treatment of Lyme Disease Complex.  The reasons for these variations will be discussed further below.  (A good article encompassing the ILADS protocol written by Burrascano called “Diagnostic Hints and Treatment Guidelines for Lyme and Other Tick Born Illness. 2008 revision)


Unfortunately, there are some people who don’t have complete recovery from a IDSA “short” course of antibiotics.  There may be many reasons for this treatment failure.  Most likely the problem is a combination of inappropriate immune response and Borrelia’s ability to evade the antibiotic treatment in multiple ways.  Some people also have other problems triggered by Borrelia that go beyond the persistence of Borrelia infection.


Borrelia can alter its antibiotic sensitivity by:

1)    The bacteria has a slow replication lifecycle which makes the antibiotics effective at a slower pace.

2)    Borrelia’s ability to hide inside you in places which your immune system and antibiotics can’t reach such as tendons, nerves and vacuoles within cells.

3)    Borrelia can alter it’s shape.  Borrelia can be in a spiral or ball shape, and these forms are differently sensitive to antibiotics.


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

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

Antibiotics kill or stun a large percentage of the infection.  We assume your immune system will destroy the remaining bacteria.  This is the reason people with HIV/AIDS, cancer, autoimmune diseases or the elderly are more susceptible to infections without recovery.  If the combination of your immune system’s function and antibiotic efficacy aren’t enough to entirely kill Borrelia from your system, then it’s possible it will remain a persistent infection.

An argument between IDSA and ILADS is if the consequences of a Borrelia infection are from “post lyme related consequences” or a persistent Borrelia infection.  There are studies that show Borrelia can be persistent after aggressive treatments in dogs, mice, and monkey

I think it’s silly to think the same isn’t possible for humans!

How Borrelia evades treatment.

One theory on how Borrelia can evade immune response is about antibodies.  Your immune system has a choice between the way it can fight as infections.  Either you can fight an infection by your immune cells eating the infection (cell mediated immunity) or you can make proteins that stick specifically to that infection (antibody).  The balance between antibody and cell mediated immunity is critical and each arm of this immune system is effective against certain infections.  Ideally our immune system should attack Borrelia with antibodies, as they are likely somewhat protective against Borrelia.  Cell mediated immunity is NOT an effective attack against Borrelia because Borrelia can live inside the cells that try to eat and destroy the BorreliaBorrelia has the ability to reduce antibody production and increase cell mediated immunity.  The ability of Borrelia to alter immune function compounds matters.
How to Test for Borrelia

How to Test for Borrelia

Testing for Lyme disease is controversial and potentially inaccurate.  It’s estimated that 35% of Lyme disease cases are missed with standard testing.  There is NO follow-up test to determine if the treatment has been successful at the time of finishing the treatment. I strongly suggest getting appropriate testing, which includes an IgG and IgM Western Blot  (for example from Igenex) AND also looking for the infection!  Please keep in mind the testing isn’t 100% accurate! You should read more about testing on IgeneX’s website.

The Problem with IDSA testing criteria is this.  The two tier testing says first do an ELISA blot and then do a Western blot.  The ELISA is a generalized “do you have antibodies to Borrelia” test.  The western blot is then “do you have antibodies to this part of Borrelia? How about this part of Borrelia?”  Both of the tests are antibody tests.  The IDSA guidelines require a strong antibody response.  The problem is that Borrelia may have the ability to stop people’s immune system from attacking with antibodies and switch your immune system toward a cell mediated immune response.  This immune system switch makes the IDSA criteria tests NEGATIVE because the bacteria tricked your immune system.  There are logical solutions to this problem.

1)    Still test for Borrelia antibodies.  But know this test tells you if your immune system has been exposed to Borrelia AND is can react correctly with an antibody response.  A negative only means no antibodies (either no exposure, or exposure and incorrect immune response.

2)    Test for cell mediated reactions as well.  This is how you test for Tuberculosis (Tb).  Because Tb is fought with a cell mediated immunity reaction.  If you fight Borrelia with cell mediated immunity, you have been tricked by the infection and the treatment MUST be more aggressive and WILL be more difficult.  This type of testing can be done but it’s more expensive.  Someone could develop a PPD test for Borrelia just like one for TB and that would be a great help.  I hope that someone out there is reading this!  For now cell mediated immunity testing is one by companies such as Neurosciences in the panel called “my lyme immuneID4

3)    TEST FOR THE BORRELIA INFECTION!  This is my first preference.  Why test for your immune system’s opinion of an infection 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 a urinary tract infection, meningitis, strep throat or many other types of infection you would look for the infectious organism, not your immune system’s opinion.  Yet with Borrelia, we insist on asking our immune system…which is duped by the infection.  Go figure (This is another major bone of contention between IDSA and ILADS).  There are multiple ways to detect the whole living organism, pieces of protein or DNA from Borrelia.  Some are more accurate than others.  I prefer an antibiotic challenged urine dot-blot PCR panel test through IgeneX  but there are multiple choices out there.  Why don’t people use these other tests?  Why not culture if you can find the living organism…?  Well here is the IDSA guideline quote about why you don’t use cultures

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.  Yup.  That’s it!  That’s the reason the International Disease Society uses in order to ignore or avoid doing culture testing in the IDSA guidelines.


You want to know what I think is cumbersome and expensive?  Having an infection that changed your immune response to make the infection undetectable by IDSA criteria.  Then having to live with it while a string of IDSA doctors tell you you are crazy, depressed, emotional, faking it and making up a disorder.  And while you jump from doctor to doctor to hear that you don’t have lyme, which may be the wrong translation of an antibody test for Borrelia.  You’re getting autoimmune diseases triggered, brain damage, muscle damage and generally falling apart.  That’s cumbersome…and expensive.


If you are a doctor, you want an answer yesterday.  Doctors want lab results by the time you utter the sentence “I want lab results.”  I sure do!  I LOVE LABS!  Yes, it may take three to six weeks to get test results on a culture or antigen detection.  That is bulky and cumbersome because you want to know the answers immediately.  But, that doesn’t make the test wrong, it makes the test slow.  Treat while you wait if you have the clinical suspicion of Lyme Disease.  Wait for results.  Treat the right thing.


I can’t even count anymore how many times a patient of mine went to an IDSA doctor and they said the patient didn’t have Lyme.  Banged their hand on the desk and insisted the patient didn’t have lyme.  Kicked the patient out of the office because they don’t have Lyme.  Generally threw a temper tantrum that the patient didn’t have lyme.  Some didn’t.  But guess what?  More often than not they do!


I use the Igenex urine dot-blot PCR panel test frequently because the test finds Borrelia pieces in your urine after a dose of antibiotics.  This test is also not accepted by IDSA criteria.  The test is designed to find either DNA or protein from Borrelia in your urine.  When you take antibiotics for 6 days, after not antibiotics for 6 weeks, there tends to be a large die-off of Borrelia.  This test is most accurate during the first several days of an antibiotic treatment in a long standing Borrelia infection.  So, I reserve this test for a person who hasn’t done antibiotics in 6 weeks.  Then the patient uses antibiotics as a “therapeutic trial” of treatment while looking for the organisms in their urine.  My take is, if you pee out Borrelia pieces, you likely have the infection.  The IDSA take on the urine dot-blot PCR panel test?  Not acceptable, not admissible…doesn’t exist.  With a positive urine dot-blot PCR panel  in hand a IDSA doctor will say “Do an ELISA and then a western blot to see if your immune system makes antibody to Borrelia.  No substitutions, no exceptions.”


If you had the classic “bulls eye rash” (erythema chronicum migrans), you can be certain you have been exposed to Borrelia, but only 50% of people at most get the rash (and no one who took the prophylactic 200mg Doxycycline once at the time of the bite)!  Other indicators of a Borrelia infection include Bell’s Palsy, migrating muscle and joint pains, especially when in concert with heart problems and neurological problems.  These symptoms are very good indications you have Borrelia.


I feel it’s necessary to know if you have Borrelia.  Assuming you have Lyme disease because you have symptoms isn’t advisable.  Your condition could be a multitude of things.  Having a history a positive diagnosis for Borrelia, herx reactions during treatment or an ECM rash is a likely indicator it’s Lyme.  Don’t assume lyme!  Don’t treat all joint and muscle pain with fatigue as Lyme.  Know first.  Even if you know you have Borrelia, don’t assume it’s Lyme!  It could be a co-infection or other problem causing your symptoms and Borrelia is aggravating that other condition.


Using tests that aren’t acceptable to IDSA criteria is the method I suggest to find the Borrelia organism.  A positive ISDA diagnosis is another way to diagnose Borrelia.  I strongly discourage treating issues as Lyme that aren’t Lyme.  It’s toxic, a waste of antibiotics, way too expensive and it’s plain old negligence, malpractice and ignorant!  I know this paragraph is silly but how many “Lyme treatments” were preformed on people that have problems that aren’t Borrelia?  Can’t say.  I bet it’s a lot!


We’ve learned so much about HIV/AIDS changing immune systems.  We have technology that can test immune system dysregulation.  With all the knowledge we have, it’s frustrating the IDSA can’t think of an infection and immune system dysregulation at the same time!
IDSA protocol
Ilads Criteria
How to test for Borrelia
Symptoms of Borellia and Co-infections
Goals of Treatment

I use natural treatments for most conditions.  But I feel antibiotics are an integral part of successful treatment for Lyme disease.  However, I do not believe antibiotics are enough for everyone.  Some cases of Lyme Disease require longer courses of antibiotics and supplemental treatments to facilitate the action of the antibiotic, and reduce the effects the Borrelia and co-infections.  Most people haven’t test if their immune system can recognize Borrelia, so I feel that aggressive treatment is a good idea initially.


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!


 I’ve seen multiple people have severe inflammatory symptoms (optic neuritis, MS, Auditory neuritis, vertigo) get treated with steroids.  Lyme wasn’t properly diagnosed, and those people become severely damaged from the medical immune suppression that allowed Borrelia to worsen and cause more damage.  In each of these cases, we later found proof of the organism in the person’s system.  Accurate diagnosis is something that should have been done before treatment!  Sadly, the emergency nature of some of the Borrelia symptoms cause extreme treatment without time for a cumbersome and expensive test to get in the way.


As I mentioned, I consider antibiotic use for Lyme critical, 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 more critical.   Especially if you’ve been unsuccessfully treated or living with chronic Lyme disease.  Treating adrenal and thyroid health, heavy metal toxicity, immune balance, nerve function, heart health, mental function and many other aspects of the Lyme Disease Complex is necessary to reduce and resolve your symptoms.  I suggest using a Lyme literate doctor to help you with this complicated treatment. Referrals for “lyme literate” physicians may be obtained through (CREATE LINK).  I feel integrative doctors, like Naturopaths, are uniquely suited to treat the entire disease complex.  A MD or DO may be necessary for insurance coverage, specific testing or prescriptions that aren’t available to certain medical licenses.  Therefore a team of a integrative lyme literate specialists is ideal for certain difficult chronic extreme cases, if not all cases.


A common issue in treating Lyme is the Herxheimer reaction.  Herx reactions are cyclic changes of your symptoms through the treatment.  It’s not specifically what the symptoms are, it’s that the symptoms cycle.  This is due to the organisms dying off, related to Borrelia’s lifecycle and your immune response at the same time.  Whether you are treating Lyme disease with antibiotics AND/OR natural treatments, you should expect to get worse and better, cyclically.  This is the process before you get and stay better.  The Herx reaction can be used to guess how the outcome of the treatment is going to be.  People who Herx less and feel better faster, tend to stay well.  Often the Herx reactions come and go.  One way to know your treatment is done, is that you don’t have Herx reactions for 2-3 months while on treatment.  You may be treating yourself for 6 months to 1 year, or more, before you get to this point!  An ILADS doctor will treat you beyond the point you have Herx reactions.

Herx reactions are one of the indications that you do have an Borrelia infection.  Monitoring and tracking your herx reactions is essential.
Symptoms of Borrelia and Co-Infections

Symptoms of Borrelia and Co-infections.

Symptoms that are common to each and infection that may Herx.


Acute symptoms  which usually occur 7-10 days:  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 arthralgi­as, stiffness, arthritis, myalgia, 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, cranial nerve disturbances (facial numbness, pain, tingling, palsy or optic neuritis), headaches, lightheadedness, dizziness.




Bartonella: Bartonella Henslae the most common but there are 26 species and two to four are tested  with arguably around 30% accuracy.

Extreme Flu like symptoms.  Fever, chills, sweats, high liver enzymes, High liver function tests.  The most common symptoms include extreme MUSCLE AND NERVE symptoms.  SOLE OF FEET PAIN and brain fog.

Central nervous system symptoms: predominant: encephalitis, muscle twitches, tremors, insomnia, seizures, anxiety, mood swings, headaches, musculoskeletal, migratory joint pain, synovitis, sore soles of feet

Skin symptoms: Purple lines on arms and flanks, tender sub Q nodules on out thighs and upper arms.

Gastro intestinal: : Hepatitis: Inc Liver function tests, Gastritis (esp. non-h. pylori), mesenteric adenitis, splenomegaly



Babesia: Microti and duncani most common, 14 sub species.  Parasite like malaria.

Onset 1-6 weeks acute and chronic months to years.  FISH test is the first to do with 30% accuracy.


Rapid onset 1-6 weeks later with a EXTREME flu like symptoms including chills, fever, drenching sweats, disorientation, liver and splenomegaly and air hunger.

Chronic symptoms: slow onset, drenching sweats esp. at night, flushes w/heat, temp instability, air hunger, occipital and frontal headaches, pressure headaches, cognitive and memory problems, dizziness, tipsiness.  Autonomic nervous system disruption:  Tachycardia, PVC, Orthostatic HTN, Shortness of breath.

Most common: Night sweats , facial flushing, muscle pain, insomnia



A note about inflammation.  We tend to think of inflammation as pain, redness, swelling, etc.  Please don’t think of inflammation like that anymore.  Those are symptoms of the inflammatory process.  Inflammation is the conversation your immune system is having.  It’s ESSENTIAL to have inflammation.  I’ve been describing Borrelia’s ability to alter your immune system by switching it from antibody production to cell mediated immunity.  This process of immune modulation is changing the conversation your immune system is having to create inflammation.

Here’s the part that’s hard to read…

Who told you Borrelia is killable?

It might not be.  It takes a combination of your immune function and antimicrobial treatments to kill it.  If you don’t have the appropriate immune response, it’s not kill-able.  The goal of treating Borrelia, in this case is to get the infection as minimal as possible so you can have a healthy and productive life.  Ideally without either your immune system or the bacteria causing irrevocable damage to you in the process.  Most Lyme literate doctors know it’s not kill-able.  It’s about management.  In my treatment, I always intend to kill the infection first with well planned thorough integrative treatment.  But I also say from day one…this may not be fixable.  Not everyone can kill it. You may find yourself at a point that you have to manage it.  What management means is also debatable.
Goals of Treatment

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

Here’s what a comprehensive Borrelia treatment should include

1)Antibiotics appropriate to the disease state

2) gut bugs to help protect the organisms in your gut

3) Glutamine to help protect your gut lining from damage

4) A biofilm treatment

5) Immune modulators toward antibody production

6) Herbs and other treatments that may also kill Borrelia (teasel, scutellaria biacalensis, guiacum, zhang formula)

7) supportive treatments: Adrenal, thyroid, heavy metal, fungal etc

8) Appropriate diagnosis and lab monitoring through the entire process to reduce damage as much as possible.

Do I think I should be your Lyme doctor?  Yes. I did my thesis on Lyme in school and have studied it quite extensively.  I have tools that are out of reach of other doctors like herbal mixtures, Nutraceutical, Bryon White formula, Zhang formula and non IDSA tests.  There are some drugs I can’t prescribe that you may need.  It depends on the severity of your symptoms.  It takes a personalized approach to figure out what it’s going to take to manage your symptoms, modulate your immune system and treat the infection.  I think you should have an appointment with me and hear what I have to say.  The treatment is based on you, tailoring the treatment specifically to your situation and it’s integrative and comprehensive approach.  You may not like that I said it’s unkillable.  It doesn’t matter what I say. If the IDSA and ILADS could get together and agree on three points then I think the political nightmare would be over.  The three points are

1)   Borrelia changes your immune system’s conversation including antibody production, antibody class switching, cell mediated immunity and inflammatory chemicals.

2)   It MIGHT be a persistent infection in some people, as it has been shown in multiple studies.

3)   Testing needs to be expanded and accurate detection of the actual Borrelia infection is critical, not optional.

Then we could get to the point that Borrelia is a treatment problem and not a political problem.

I think one of the problems with the ISDA guidelines is because an infectious disease specialist uses antibiotics (and other critter killing treatment) and can not alter the immune system in the process.  They can not alter the immune system knowing it takes a healthy immune response to kill that infection.   The doctor that treats your immune system is a rheumatologist.  Rheumatologists use tools to suppress or shut down parts of your immune system.  You can’t suppress an immune system when you fight an infection.  So, what we need to treat Borrelia is an Infectious Disease Rheumatologist and that doctor would have 2 sets of tools that aren’t compatible.

Here is my opinion about the cure to Lyme Disease

(the problems, the controversy, everything)

I’m putting this part of this article out there is dire hopes that it’ll make it to a pharmaceutical developer.  If it does…yes, I want to consult!  Hire me!  This type of research is what I used to do at Harvard before my career as a naturopath (although not specifically for Borrelia.)   I know this is kind of jokey, it’s not.  I really do believe this is the solution to the entire problem!


Find the mechanism that Borrelia uses to switch our immune system’s conversation from antibody production to cell mediated immunity (Th2->th1).  Create a drug or monoclonal antibody that can block that chemical so your immune system doesn’t get switched.  Increase antibody production with a drug or immunotherapeutic (herbal, IL-10, IL-4, etc).  Concurrently use antibiotics to kill the infection, block immune modulation and inject Borrelia monoclonal antibodies.  Likely this will take a chronic Borrelia infection to a place of easy symptoms free management.  For the drug companies out there… this drug will be useful for people with antibody production problems as well.  You could use the way that Borrelia switches our immune system to work on things like allergies, antibody dominant autoimmune diseases and immunoglobulin overproduction disorders.  I hope this paragraph finds the right place.  Please get in touch with me so I can help and capitalize in any way from this terrific idea J.  Remember, this is a copy written article!
IDSA protocol
Ilads Criteria
How to test for Borrelia
Symptoms of Borellia and Co-infections
Goals of Treatment

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