Lyme Borrelia Group (Lyme Disease) Nucleic Acid Amplification Testing (NAAT): Optimal Testing Recommendations

  • If a clinical diagnosis cannot be made based on the presence of erythema migrans (“bulls-eye” rash), serologic testing is the diagnostic method of choice for Lyme disease per the Centers for Disease Control and Prevention (CDC)
  • Borrelia Species by NAAT (e.g., PCR) should not be used as a first-line test for Lyme disease.
  • Borrelia Species by NAAT can be used to test synovial fluid or tissue in seropositive patients, if the diagnosis of Lyme arthritis is being considered but treatment decisions require more definitive information.

Guidelines for Test Utilization

What does the test tell me?

Positive results indicate the presence of the Lyme Borrelia group nucleic acids; however, direct detection of the Lyme Borrelia group by NAAT has poor clinically sensitivity outside of detection of Borrelia from synovial fluid. In all cases, CDC recommends a two-tiered approach of a screening enzyme immunoassay followed by confirmatory testing either with a western immunoblot or a second enzyme immunoassay for first-line testing. [back to top]

When should I order this test?

This test should be ordered for patients who are suspected of having Lyme arthritis and seropositive but whose history of past Lyme disease complicates the ability to diagnose on that basis. [back to top]

When should I NOT order this test?

Do not order this test for asymptomatic patients, patients with skin lesions compatible with erythema migrans, and patients with positive Lyme antibody testing except the condition in Section 4, or as a “test of cure” after treating for Lyme arthritis. [back to top]

How should I interpret the result?

When detected, nucleic acids from Lyme Borrelia group organisms may be assumed to be present. Nucleic acid positivity can persist for weeks to months after successful treatment of Lyme arthritis. Negative results do not rule out presence of the organism. [back to top]

Is the test result diagnostic/confirmatory of the condition? If not, is there a diagnostic/confirmatory test?

Yes, if positive prior to antimicrobial therapy and consistent with clinical presentation of the patient. [back to top]

Are there factors that can affect the lab result?

Clinical sensitivity for Borrelia DNA in cerebrospinal fluid and blood is not sufficient for clinical utility. [back to top]

Are there considerations for special populations?

Not applicable. [back to top]

What other tests might be indicated?

Lyme antibody testing should be performed as the first line test. [back to top]


Carroll KC, Landry ML, McAdam AJ, Patel R, Pfaller MA, Richter SS. Manual of Clinical Microbiology.  Washington, DC: ASM Press, 2019. 

Lantos PM, Rumbaugh J, Bockenstedt LK, Falck-Ytter YT, Aguero-Rosenfeld ME, Auwaerter PG, et al. Clinical Practice Guidelines by the Infectious Diseases Society of America (IDSA), American Academy of Neurology (AAN), and American College of Rheumatology (ACR): 2020 Guidelines for the Prevention, Diagnosis and Treatment of Lyme Disease. Clinical Infectious Diseases. 2021;72:e1–48.

Mead P, Petersen J, Hinckley A. Updated CDC Recommendation for Serologic Diagnosis of Lyme Disease. MMWR Morb Mortal Wkly Rep. 2019;68:703. 

Last reviewed: February 2022. The content for Optimal Testing: the Association for Diagnostics & Laboratory Medicine’s (ADLM) Guide to Lab Test Utilization has been developed and approved by the the Academy of Diagnostics & Laboratory Medicine and ADLM’s Science and Practice Core Committee.

As the fields of laboratory medicine and diagnostic testing continue to grow at an incredible rate, the knowledge and expertise of clinical laboratory professionals is essential to ensure that patients received the highest quality and most useful laboratory tests. ADLM’s Academy and Science and Practice Core Committee have developed a test utilization resource focusing on commonly misused tests in hospitals and clinics. Improper test utilization can result in poor patient outcomes and waste in the healthcare system. This important resource geared toward medical professionals recommends better tests and diagnostic practices. Always consult your laboratory director to make sure these recommendations are appropriate for your patient population.