Using PCR Testing for Lyme Disease

by lmatthews on June 12, 2012

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.

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