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Polymerase chain reaction is often used for detection of Borrelia burgdorferi in biological specimens. It has been suggested that polymerase chain reaction may be used as a surrogate marker of cell viability. To test this premise, B. burgdorferi cultures were treated with the antibiotic, ceftriaxone, and aliquots were cultured for cell viability and tested by polymerase chain reaction. Ceftriaxone treatment abrogated the ability to subculture B. burgdorferi by three days post-treatment. In contrast, positive polymerase chain reaction results were obtained for up to 56 days after antibiotic treatment. These findings indicate that positive polymerase chain reaction results do not provide proof of bacterial cell viability in vitro.