Borrelia Species DNA, Real-Time PCR, with Reflexes, Blood
Real-time PCR for Borrelia species DNA in whole blood detects B. burgdorferi sensu lato and B. miyamotoi nucleic acid, offering molecular confirmation during early infection before antibody seroconversion. Sensitivity is modest due to low-level, transient bacteraemia; a positive result confirms infection, while a negative result does not exclude it.
2
Biomarkers
Blood (whole blood)
Sample
3–5 business days
Turnaround
No
Fasting
What is the Borrelia PCR test?
The Borrelia Species DNA, Real-Time PCR, with Reflexes test uses nucleic-acid amplification to detect DNA of Borrelia burgdorferi sensu lato and Borrelia miyamotoi directly in whole blood. It is ordered when a practitioner suspects early Lyme disease or B. miyamotoi infection and seeks molecular confirmation before antibodies develop, or when serological results are equivocal and direct pathogen detection might clarify the diagnosis. Molecular testing complements rather than replaces serology in the Lyme diagnostic algorithm. Because spirochaetal bacteraemia is low-level and intermittent, the sensitivity of blood PCR is limited — reported at twenty to fifty per cent in early localised disease and somewhat higher during early dissemination, but falling once the organism is sequestered in tissue. The reflex component typically triggers additional species-level or genospecies discrimination when initial screening detects Borrelia DNA, enabling the laboratory to report whether the signal corresponds to Lyme or relapsing-fever group organisms. Practitioners use this test in the narrow window when serology is not yet informative and when the pre-test probability is high enough to justify its modest sensitivity.
What does the Borrelia PCR test measure?
Borrelia burgdorferi sensu lato comprises the genospecies responsible for Lyme borreliosis in North America and Europe. The spirochaete circulates in blood primarily during early disseminated infection, before immune clearance reduces bacteraemia to levels typically below the threshold of direct detection. DNA amplification by real-time PCR targets conserved borrelial genes — often the outer surface protein A (ospA) or flagellin — to identify spirochaetal nucleic acid when organisms are present in the circulation or tissue.
Direct detection of Borrelia DNA offers the possibility of confirming active infection without waiting for antibody seroconversion, particularly in the first few weeks after tick exposure when serological tests remain negative. Because bacteraemia is low-level and transient, sensitivity in whole blood is modest and varies by disease stage; detection is highest during early disseminated infection and drops sharply once the organism localises to tissue. A positive result confirms infection; a negative result does not exclude Lyme disease, and the test is adjunctive to serology and clinical assessment.
Borrelia miyamotoi is a relapsing-fever group Borrelia transmitted by the same Ixodes ticks that carry B. burgdorferi but causes a distinct clinical syndrome characterised by fever, headache, and — unlike Lyme — rarely erythema migrans. The spirochaete circulates at higher density during febrile episodes, making nucleic-acid amplification more sensitive than for Lyme borreliosis. PCR targets genes specific to the relapsing-fever group to discriminate B. miyamotoi from Lyme Borrelia.
B. miyamotoi infection is increasingly recognised in tick-endemic regions and can mimic other febrile illnesses; standard Lyme serology does not detect it. Real-time PCR is the primary diagnostic tool during the acute febrile phase, when spirochaetal load in blood is highest. Sensitivity falls between fever episodes and after antibiotic therapy, so clinical suspicion and timing of the draw are critical. A positive result establishes the diagnosis; a negative result in a patient between relapses or after treatment does not rule out infection.
Why is the Borrelia PCR test ordered?
- Evaluation of suspected early Lyme disease in the first two to four weeks after tick exposure, before IgM and IgG antibodies reach detectable levels
- Investigation of erythema migrans in a patient from an endemic area when the rash is atypical or when confirmation is required before prolonged antibiotic therapy
- Assessment of acute febrile illness with headache, myalgia, and tick exposure in a region where B. miyamotoi is endemic, particularly if standard Lyme serology is negative
- Clarification of equivocal or discordant serological results in early disseminated Lyme disease, interpreted alongside two-tier serology and clinical findings
- Suspected relapsing fever-like syndrome with recurrent fever episodes in a patient with Ixodes tick exposure, where B. miyamotoi is in the differential
- Evaluation of possible early neuroborreliosis or carditis when urgent molecular confirmation might guide immediate therapy, though cerebrospinal-fluid or tissue PCR is preferred for localised manifestations
Sample collection and turnaround
Sample type
Blood (whole blood)
Fasting required
No
Collection method
Venipuncture at patient service centre
Turnaround
3–5 business days
Collection notes
Phlebotomy at Quest draw site; whole blood collected in EDTA (lavender-top) tube. Draw before starting antibiotics whenever possible, as even short-course therapy can clear detectable DNA within one to two days. Refrigerate and transport promptly to preserve nucleic-acid integrity.
Specimen requirements
Minimum 3 mL whole blood in EDTA. Do not freeze. Maintain cold-chain during transport; DNA degradation reduces sensitivity. Note date and time of collection relative to symptom onset and any antibiotic exposure.
What can affect Borrelia PCR results?
Spirochaetal density in blood peaks during early disseminated infection; sensitivity is lower in early localised disease (first week) and falls sharply once the organism leaves the bloodstream, so a negative result days or weeks after symptom onset does not exclude infection.
Even a few doses of doxycycline or amoxicillin can clear detectable DNA from blood within one to two days, so the sample should be drawn before starting antibiotics whenever possible.
Borrelia bacteraemia is transient and often below the limit of detection; PCR on a single blood draw has inherently modest sensitivity, and a negative result is common even in true infection.
Well-designed real-time PCR assays target conserved Borrelia genes and discriminate Lyme from relapsing-fever genogroups, but laboratories should validate against other spirochaetes (Treponema, Leptospira) to minimise false positives.
Whole-blood specimens for PCR should be collected in EDTA and processed or refrigerated promptly; delays and temperature excursions can degrade spirochaetal DNA and reduce sensitivity.
European B. afzelii and B. garinii may be detected by PCR panels designed for sensu lato detection, but target-gene conservation differs; confirm the assay covers relevant local genospecies.
What do Borrelia PCR results mean?
Elevated
Not applicable — this is a qualitative (detected/not detected) assay, not a quantitative marker.
Normal
Borrelia DNA not detected. This is the expected result in an uninfected individual. Interpretation depends on disease stage: a negative result does not exclude Lyme or B. miyamotoi infection, because sensitivity in blood is modest and bacteraemia is intermittent. Serology remains the cornerstone of Lyme diagnosis, and clinical assessment guides the decision to treat empirically when suspicion is high.
Reduced
Not applicable.
Note: A positive PCR result — Borrelia DNA detected — confirms active or very recent infection and should prompt appropriate antimicrobial therapy. The reflex component identifies whether the DNA corresponds to B. burgdorferi sensu lato (Lyme) or B. miyamotoi (relapsing-fever group), guiding both treatment and epidemiological reporting. A negative result is common even in true disease; sensitivity in whole blood is far lower than that of two-tier serology after seroconversion, so PCR is adjunctive and most useful in the narrow pre-seroconversion window or when serology is equivocal. Always correlate molecular findings with clinical context, exposure history, and serial serology.
Frequently asked questions
PCR detects spirochaetal DNA directly in blood and is most useful in the first few weeks after tick exposure, before antibodies develop. Serology detects IgM and IgG antibodies and becomes positive around three to four weeks; two-tier serology remains the diagnostic cornerstone once seroconversion occurs, because PCR sensitivity in blood is modest.
How to access the Borrelia PCR test
The Borrelia PCR reference page is free and open to all practitioners. Create a free practitioner account to see pricing, save tests to your list, and generate requisition forms. Verification takes 1–2 business days.
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Published: October 7, 2026
Last reviewed: October 7, 2026
- Wormser GP, et al. The clinical assessment, treatment, and prevention of Lyme disease, human granulocytic anaplasmosis, and babesiosis: clinical practice guidelines by the Infectious Diseases Society of America. Clin Infect Dis. (2006)
- Sanchez E, et al. Diagnosis, treatment, and prevention of Lyme disease, human granulocytic anaplasmosis, and babesiosis: a review. JAMA. (2016)
- Krause PJ, et al. Borrelia miyamotoi sensu lato seroreactivity and seroprevalence in the northeastern United States. Emerg Infect Dis. (2014)
- Molins CR, et al. Collection and characterization of samples for establishment of a serum repository for Lyme disease diagnostic test development and evaluation. J Clin Microbiol. (2016)
- Marques A. Revisiting the Lyme disease serodiagnostic algorithm: the momentum gathers. JAMA Netw Open. (2020)
This content is for licensed healthcare practitioners only and does not constitute medical advice. Clinical decisions should be based on the full clinical picture and not on any single test result.