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Using PCR Testing for Lyme Disease

pcr test lyme disease borrelia dna genome

The Lyme disease bacteria genome - but PCR cannot differentiate between live and dead bacteria.

The CDC recently released information guiding physicians through the use of PCR testing for Lyme disease in light of the increased reliance on this type of Lyme disease test in practice. Dr. Christina Nelson, Medical Officer in the Bacterial Diseases Branch of the Centers for Disease Control Division of Vector-Borne Disease talked about polymerase chain reaction assays and their use in diagnosing Lyme disease and monitoring the progress of treatment.

Lyme Disease Tests

Lyme disease tests include the ELISA and Western Blot serological tests as well as immunofluorescent assays (IFAs) and PCR tests. The latter has a number of advantages over serological tests as it can directly detect the presence of the Lyme disease bacteria rather than relying on the immune system’s response to the antigen. As such, PCR tests can be used much earlier than those Lyme disease blood tests which rely on sufficient concentration of antibodies to trigger detection.

PCR Lyme Disease Test Limits

Limitations of PCR testing also exist, however, including an inability to differentiate between bacteria which are dead and those which are still alive and active in the body. Laboratory contamination is also an issue and can lead to false positives in Lyme disease testing. Overall, the CDC does not recommend PCR testing as a useful tool in Lyme disease diagnosis and when you look at the results of PCR tests from patients with active Lyme disease infection it is easy to see why.

PCR Unreliable

The Lyme disease bacteria, Borrelia burgdorferi, enters the body through the skin via tick bite and gradually disseminates into the surrounding tissue and general circulation. The bacteria likes to pool in collagen-rich connective tissues but may also concentrate in the heart, central nervous system, the liver, and other organs or systems. Spirochaetes are thought to remain in the blood in large concentrations only briefly, after which they will make camp in the body’s tissues, particularly larger joints such as the knees or shoulders. The concentration of bacteria in the blood is usually low, therefore, making PCR testing unreliable for anything but early detection of Lyme disease shortly after it begins to disseminate.

Finding Lyme Bacteria

According to the CDC, PCR detects Borrelia DNA in the blood of less than half of patients in the early stages of Lyme disease, at the time when the erythema migrans rash is present. A month after the first symptoms of Lyme disease arise, PCR testing becomes practically useless as spirochaetes are no longer found in the blood. Testing cerebrospinal fluid using PCR methods is equally problematic as only a third or so of patients with acute neuroborreliosis, and even less of those with later stage neurologic Lyme disease have a positive PCR test for Borrelia DNA.

Lyme Arthritis and PCR Testing

Testing synovial fluid using PCR is helpful, however, as the bacteria concentrate in the joints and cause symptoms of Lyme arthritis. This method of testing is useful in research into Lyme disease in order to monitor treatment response in patients with confirmed Lyme arthritis. Synovial fluid testing with PCR is not a common, or recommended diagnostic method, however, as too little is known about its sensitivity in such cases. More recent research suggests that bacterial remnants may be responsible for ongoing Lyme disease symptoms, even after active infection is eradicated.

Lyme Disease Rash and PCR Testing

Using PCR testing for skin biopsies is largely frowned upon as patients with the erythema migrans Lyme disease rash are usually diagnosed based on the rash and symptom history alone, without the need for such testing. No PCR-based Lyme disease tests are currently approved in the US by the FDA and ELISA plus Western Blot testing remains the primary method of diagnosing Lyme disease. In many cases these laboratory tests should be considered supplemental support for a diagnosis of Lyme disease, with the symptom history, clinical signs, and exposure to ticks or recorded tick bites being sufficient for a Lyme disease diagnosis.

PCR Testing – Unreliable for Lyme Disease

In the event that an inexperienced physician decides a patient does not have Lyme disease on the basis of a negative PCR test, it may be helpful to point them to the CDC guidelines on this matter, or seek a more Lyme literate medical doctor to either truly rule out Lyme disease infection or access appropriate treatment. PCR testing for Lyme disease may have advantages over serological tests in some circumstances but it is far from foolproof in Lyme disease diagnosis.


Aguero-Rosenfeld ME, Wang G, Schwartz I, Wormser GP. Diagnosis of Lyme borreliosis. Clin Microbiol Rev. 2005;18:484-509.

Li X, McHugh GA, Damle N, Sikand VK, Glickstein L, Steere AC. Burden and Viability of Borrelia burgdorferi in skin and joints of patients with erythema migrans or Lyme arthritis. Arthritis Rheum. 2011;63:2238-2247.

{ 2 comments… add one }
  • Kelly Clover December 17, 2012, 6:43 pm

    I am deeply bothered by the actions of a so-called infectious disease specialist in San Angelo
    who refused to accept the results of a PCR test as evidence of likely Lyme disease. How can you
    just dismiss the finding of borrelia DNA fingerprints? I have long suffered from a large number
    of symptoms suggesting the possibility of borrelia infection.
    The real problem however is with the Centers for Disease Control. The CDC continues to
    pump out a massive amount of propaganda, misinformation, and outright lies. The CDC
    stubbornly refuses to admit the tests it recommends results in huge numbers of seriously ill
    people being denied treatment. They continue to peddle the lie that PCR tests are never clinic-
    ally useful.
    The CDC has long peddled the outright lie that Lyme disease is confined to a small geo-
    graphic region. This results in huge numbers of people going untreated for their Lyme disease
    because their doctors are badly misinformed. The CDC continues to peddle the lie that Lyme
    disease is always very easy to diagnose: Just look for tick bites and a bull’s eye rash. This re-
    sults in huge numbers going without diagnosis or treatment because their doctors don’t under-
    stand that you can have Lyme without ever seeing any ticks. The CDC continues to peddle the
    lie that Lyme is very easily cured with only short-term antibiotics. This results in huge numbers
    of people receiving hopelessly inadequate treatment.
    The CDC is far and away the number 1 enemy of those who suffer from this terrible disease.

  • Kelly Clover January 25, 2013, 6:07 pm

    A petition to get President Obama to invalidate the outragous IDSA Lyme disease diagnosis
    and treatment guidelines is currently being circulated on the internet. It’s imperative that we get
    as many signatures as possible as quickly as possible. Information regarding how to get your name added to this petition is available at Jenna’s Lyme blog. I have no affiliation with Jenna
    Smith’s blogs. I am simply doing everything in my power to correct a grave injustice done by our
    government which has severely restricted treatment options for those with this ailment and
    caused many doctors to refuse treatment.

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