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James Schaller, MD, MAR, DABPN, DABPM

A Guide to Understanding a Lyme disease Western Blot: An Evaluation of Diagnosis Practice and the Clarity of Lab Testing

James Schaller MD

This month millions of people on earth will be told they do not have Lyme disease. The reason they will hear this conclusion is because they do not know how to read a key test in diagnosis--the Western Blot.

Some medical societies and government health agencies have very unusual and incorrect ways of reading Western Blots. And the approach to determining a positive is as casual as a show of hands among a small number of physicians.

Current policy on the interpretation of this test in every inhabited continent is to follow the opinion of 0.0000375 percent of physicians such as the opinion of most Infectious Disease of America guideline creators. If a physician does not agree with this standard Model-T approach experts who read virtually nothing on these many tick infections, they defame and insult you. This is insecure fascism and anti-science, since science is always redefining the truth. Without constant re-evaluation, science and medical science dies. This week and month, many positions were expanded or changed based on new information.

western blot

When you are a medical student, intern or resident, you are still learning the basics, and one uses many “recipe books.” So if someone is short of breath,” you do b, c and e. If someone has middle belly pain you perform the following tests-- r, h and q, and finally if you have infection, you use 500 mg of a medicine for 21 days. In other words, one size dose and one type of duration of an antibiotic are “prescribed” for the entire world. So physicians who publish authoritative, heavily defended guidelines make treatment decisions for tens of millions they have never seen. Why are those who question guidelines that do not even include the routinely missed Bartonella bacteria which is immune suppressive? Oops. Where is the approach to treating FL1953? Oops.

First, the Western Blot test measures the antibodies your body makes to attack the Lyme infection.

So if we show this sideways, the 39 is one of thirteen surface Lyme products that can be tested in N. America and the flat Y shape is an antibody bonding to it. -----< <39

I will be assuming a Western Blot is from IGeneX, which is an internationally famous, tick-only lab, with seven laboratory certifications. Other massive cheap national labs process hundreds of types of tests, and millions of patients. They rarely find a positive result even in epidemic counties, including in people who have profound and advanced Lyme clinical symptoms.

However, if you have had a Western Blot done at a junk lab, please still glance at the result. Why? Because you may find, as I did with one relative, that one of the antibodies or "bands" was positive. In this relative, the band was a "fingerprint" band.” Meaning, Lyme is the only organism that makes the human body to produce this antibody. The child was positive.

Further, if you are blindfolded and touch an elephant, you may not be sure it is an elephant–perhaps this is a rhino? This is the 41 band. It is from the flagella’s, or huge stringy rods that go from the top of the spirochete to the base, and the contraction of these many flagella create movement. Due to its immense action, it is most often positive. However, the 41 antibody is not specific to Lyme, since other spirochetes have flagella. The Chinese rule out other spirochetes, and then consider it as a Lyme positive band.

Now, what if you touch this same elephant on its tusks or on its long peanut-eating tubular nose? You know it is an elephant. Period. One touch and you are certain, because these parts are very unique to this huge animal. So how does this relate to Western Blots? It you see an 18 antibody that has a positive, you have Lyme. You do not need to check any other bands, because the 18 antibody is limited to Lyme—just like a 3 foot curved ivory tusk on an elephant.

What Do the Number of Pluses Mean?

IGeneX runs 13 surface Lyme chemicals for both antibodies in the M and G class. Most other labs remove almost all the M surface chemicals apparently because less information is more scientific? Old timers have said the full number of M surface proteins caused “too many” positive Western Blots. Some labs use numbers for each Western Band blot and most seem to use a positive or “+.”

One + means you have some antibody of that type, and +++ means you have a very large amount of antibody of that type. However, Lyme ruins immune system functioning and the number of positives can go up or down depending on the style and type of treatment. People with no aggressive past Lyme treatment, should be lucky their body shows any antibodies at all, since Lyme is very good at both hiding from the immune system and hindering it. And if Bartonella is present, which is more common than Lyme, it can turn down antibodies for a wide range of infections.

Also, many people have +/- or IND findings on an antibody. This is “indeterminate or borderline. “ This means the lab tech is seeing something that is VERY CLEAR, but one of the licensing agencies refuses to allow it to be called a positive. They only want very wide results to be accepted. Further, many patients with Lyme also show high Epstein Barr labs, which I suggest means this common infection is not in check and the immune system is very weak. I do not believe one needs multiple anti-viral drugs.

Often, physicians who treat a patient, find the +/- becomes a + or even a ++. This means you now have new and clear antibodies against this part of the Lyme bacteria.

Currently, IGeneX has its own formula for interpretation. They are accountable to different laboratory regulating agencies, and in general many governments have very old views of Lyme science, and do not even have Bartonella down as a tick infection on their Lyme guidelines. They are years behind clinical medicine and following a few Ivy Tower types who use a mere 5-10 papers to determine their positions. Many government agencies like the FDA and especially state medical boards are attacking tick infection experts. These lawyer run groups are attacking the best tick infection doctors in the USA. Generally, after the board punishes some of the best tick infection doctors in their state or country, patients often counter attack the state boards and get laws passed to stop this 1984 Big Brother harassment. But these doctors are already too afraid to treat tick and flea infections such as Atypical Bartonella, Babesia duncani, FL1953 and Lyme disease.

So any government aggression against doctors sincerely and honestly listening to patient reported illness is going to decrease physicians treating Lyme disease. And doctors smart enough to use INDIRECT labs to detect the presence of Bartonella, Lyme or Babesia will not order them because they are not simplistic routine labs. Further, this hostility to very talented doctors of medicine scares thousands of doctors into avoiding treating Lyme aggressively or makes simple thinking doctors feel these progressive doctors must have been wrong. Some physicians are simple in the politics of power. We have seen the same state board abuse against physicians willing to take on a few desperately suffering chronic pain patients, e.g., the type with rotting joints who are inoperable and need rising doses of narcotics to work fulltime and keep from crying from pain. 1

Nine known [Lyme] Borrelia burgdorferi Genus species specific KDA Western Blot antibodies (bands) are common in North America testing: 18, 23, 31, 34, 37, 39, 83 and 93. A few feel Herpes can alter 31, but I feel that is rare, even if it is true. If one looks around the world, like I do in working with patients from all over the world, here are the accepted specific Bands in the world literature: 13, 14, 17, 21, 23, 24, 25, 28, 31, 34, 35, 37, 39, 47, 50, 54, 83, 84, 93 and 94.

The lab can be a junk lab that invests nothing to optimize their testing kit, but if one of these bands is positive—Lyme is usually present in a human body. IGeneX has the best Western Blot in the world. They run five blind samples from New York State every four months for the last decade and are 98% correct. No other lab has invested so much or can touch this accuracy.


Years ago when I was discussing some Ivy League options available to me, my father schooled me on his Ivy League experience and it was largely terrible despite his amazing academic capacities which had him graduating at the top of a class of thousands. He reported the education was fair, professors were not available, useless meetings were common, politics was immense—like a presidential campaign, and good medicine was “being a clone of the teachers” who had lower scores on many exams and had fair clinical skills.

Currently, the respected schools and many agencies require a weaker test called an ELISA and do not order any other test for other infections, and do not look at indirect tests. Indeed, these “experts” are clueless about the meaning of the expression of an indirect test for Lyme, Bartonella or Babesia.

So to put it bluntly, the ELISA test as a screening tool is useless, missing even the most obvious PCR positive patients with clear past histories of massive Bull’s Eye rashes, which, while not the norm, provide evidence of spirochetes.

Only one of these specific bands is needed to confirm that there is evidence of exposure to the Borrelia burgdorferi spirochete.

CDC IgM criteria have a mere two antibodies for IgM 23 and 39 and exclude the other seven Borrelia burgdorferi antibodies.

CDC IgG criteria include 18, 23, 30, 37, 39 and 93 and exclude bands 31, 34 and 83.

Why would any person ever remove useful information? Why would one dummy down a test by removing very sensitive surface proteins. It does not make sense to exclude any Borrelia burgdorferi specific antibodies, and to include only two of these antibodies in IgM. If you do this you are an utter anti-scientist.

The CDC wrongfully includes five non-specific antibodies in its Western Blot, i.e., 28, 41, 45, 58 and 66. Why exclude tests or bands that are specific, and add bands that are not specific for only Borrelia burgdorferi?

Further, one can have a CDC surveillance positive IgG Lyme Western Blot with the five non-specific antibodies without having any Borrelia burgdorferi genus species specific antibodies.

This does not make sense. And it is not rocket science. The CDC recommends that the Lyme Western Blot be performed only if there is a positive or equivocal Lyme ELISA.

So one excludes a quality Western Blot test that is not a dirty test like the ELISA? Is this a joke? Do these people understand if you miss this infection for 5, 10, 20 or 30 years it can destroy a life? This is not a mere two or three week flu. We know untreated long term syphilis is dangerous. Lyme spirochetes walk over syphilis like they are weak little ants.

So consider using the Western Blot only from labs with ten or more years of 98% accuracy on blind trials. Use the Western Blot to allow antibodies to bind to the exact fingerprint surface chemicals of Lyme spirochetes.

No one knows the exact accuracy of ELISA testing, and many physicians have seen many false negatives or routine false negative ELISA’s and “CDC positive” Lyme Western Blots. Or positive PCR (DNA) for Lyme disease and positive Western Blots, but negative ELISA's. The Lyme ELISA is trash. Any first year medical student knows a good screening test should never miss positives.

There is no tick infection POPE in any school or government agency. The nonsense that the tick that passes Lyme only passes Lyme is dated by at least 20 years. So not only do we use junk testing, we imagine the ticks that carry Lyme, only carry Lyme disease, when the sober reality is these ticks are super carriers with many bacteria, protozoa, and viruses. Many people are easily impressed with fancy titles and big name schools, and forget most of these people know nothing about the super specialization of tick and flea-borne infections. When someone clearly has no idea how to detect Bartonella besides a direct antibody test—run. When an organization has no guidelines on how to treat Mepron treatment failure—run. When a group or person rejects looking at ALL MAJOR tick borne viruses or for all possible bacteria, after a clinically serious bite—run. If the group and practitioner has never heard of FL1953—consider running. If you are told your positive Western Blot is a false positive, ask if they will agree to pay for your new hip or new hand microsurgery in the future if they turn out to be wrong? The odds are in their favor since only 25% of Lyme patients have serious joint damage.

It is one of many reasons why it is absurd that this was ever seen as a pure rheumatology disease.

The person diagnosing you has a certain style of thinking. They have ways that guide them in their decisions. Are you OK with someone following 10, 20 or 30 people? Are you or they more afraid of antibiotics or untreated bacteria? The fact is both patient and doctor bring 50 assumptions of medical knowledge to the table, and your unique situation may not be seen ever as unique, since the tables positions control reality.

NOTE: The reading of Western Blots is debated. If you want a conservative approach, please ignore this article.

• (For example, Pennsylvania, Delaware and New York are three of the leading pro-pain, anti-Lyme treatment or anti-doctor states in the USA. When my father was practicing OB/GYN in women, the useless Governor Ed Rendell with a new girl for every day did nothing when malpractice premiums were in excess of salaries! And now DE, after years of allowing criminal and impaired physicians, has turned on MD’s to be the worst state or “town” to practice in the entire USA).


J. Schaller, K. Mountjoy, A Researcher's Guide to Basic References in Bartonellosis, Babesiosis and Borreliosis or Lyme Disease: A Voluminous Citation Guide to Move Beyond Terse Guidelines And Reviews. International Infection Academic Research Press. July 2012

J. Schaller, K. Mountjoy, The Definitive Collection of Academic of Academic References on Lyme Disease and the Pathology of Borrelia. International Infection Academic Research Press. July 2012.

J. Schaller, K. Mountjoy, The Definitive Collection of Academic of Academic References on Bartonella and the Pathology of Bartonellosis. International Infection Academic Research Press. June 2012.

J. Schaller, K. Mountjoy, An Extensive Collection of Academic References Focused on Emerging Babesia and Malaria. International Infection Academic Research Press. May 2012.

J. Schaller, K. Mountjoy, Checklists for Bartonella, Babesia, and Lyme Disease, 2012 edition. International Infection Academic Research Press. May 2012.

J Schaller, K. Mountjoy, What You May Not Know About Bartonella, Babesia, Lyme Disease and Other Tick & Flea-borne Infections: Improving Treatment Speed, Recovery & Patient Satisfaction. International University Infectious Disease Press. February 8, 2012.

J. Schaller, K. Mountjoy, The Checklist of Bartonella, Babesia and Lyme Disease: 2012 Edition. International Academic Infection Research Press. December 2011

J. Schaller, K. Mountjoy, A Bibliography of Selected References for Researchers and Academicians Dedicated to Tick and Flea-borne Infection Science. International Academic Infection Research Press. October 2011.

J. Schaller. Babesia 2009 Supplement and Update. Hope Academic Press. Tampa, FL. Jan. 2009.

J. Schaller. A Laboratory Guide to Human Babesia Hematology Forms. Hope Academic Press. Tampa, FL. Sept. 2008. Images derived from texts, journal papers, CDC, departments of health and other licensed labs with high reported accuracy.

J. Schaller. The Diagnosis, Treatment and Prevention of Bartonella: Atypical Bartonella Treatment Failures and 40 Hypothetical Physical Exam Findings – Full Color Edition. Volume I-II. Hope Academic Press. Tampa, FL. June 2008.

J. Schaller. Artemisinin, Artesunate, Artemisinic Acid and Other Derivatives of Artemisia Used for Malaria, Babesia and Cancer. Hope Academic Press. Tampa, FL. 2006. This is possibly one of most up to date textbooks in the English language on the leading WHO and UNICEF recommended treatment of malaria which Chinese MD’s suggest also for use with Babesia

J. Schaller, G. Burkland and P. Langhoff. “Is babesiosis a missed cause of hypereosinophilia? A five-year follow up on the first published case of Imatinib mesylate for idiopathic hypereosinophilia.” Medscape. Jan. 2007. Written at request of the former editor of JAMA who at one time was editor of 40 top medical journals.

J. Schaller. The Diagnosis and Treatment of Babesiosis for Health Care Practitioners: a Review of New Human Species, Diagnostic Options and Treatments. Hope Academic Press. (396 pages) August 2006. This is the most up to date book in the world on this international infection with new species found routinely in public access genetic databases.

J. Schaller. Bartonella and panic disorder and depression. Medscape: June:2008

J. Schaller with R. Blackwell. Fifty Issues in Chronic Untreated Tick and Flea-Borne Illnesses: Cutting Edge Diagnostic Tools and Innovative Solutions that Offer Hope. Hope Academic Press. Nov. 2013 [200 pages completed. 150 comics done].

J. Schaller. “Lyme Disease” in Encyclopedia of Plagues, Pestilence and Pandemics, J. Bryre, Ed. (Westport, CT: Greenwood Press; 2008) [Book endorsed by the NIH Director of Infectious Disease.]

J. Schaller. “Bartonella” in Encyclopedia of Plagues, Pestilence and Pandemics, J. Bryre, Ed. (Westport, CT: Greenwood Press; 2008) [Book endorsed by the NIH Director of Infectious Disease.]

J. Schaller. “Babesia” in Encyclopedia of Plagues, Pestilence and Pandemics, J. Bryre, Ed. (Westport, CT: Greenwood Press; 2008) [Book endorsed by the NIH Director of Infectious Disease.]

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