Genetic diversity of Borrelia burgdorferi in Lyme disease patients as determined by culture versus direct PCR with clinical specimens

Two hundred seventeen isolates of Borrelia burgdorferi originally cultured from skin biopsy samples or blood of early Lyme disease patients were genet ically characterized by PCR-restriction fragment length polymorphism (RFLP) typing of the 16S-23S ribosomal DNA intergenic spacer. Three major RFLP ty pes were observed. Of the cultured isolates, 63 of 217 (29.0%) were type 1, 85 of 217 (39.2%) were type 2, and 58 of 217 (26.7%) were type 3; mixtures of two RFLP types were obtained in 6.0% (13 of 217) of the cultures. Compa rison of typing of B, burgdorferi performed directly on 51 patient skin spe cimens,vith typing of cultures originally isolated from the same tissue rev ealed that a much larger proportion of direct tissue samples had mixtures o f RFLP types (43.1% by direct typing versus 5.9% by culture [P < 0.001), In addition, identical RFLP types were observed in only 35.5% (11 of 31) of t he paired samples. RFLP type 3 organisms were recovered from blood at a sig nificantly lower rate than were either type 1 or type 2 strains. These stud ies demonstrate that the genetic diversity of B. burgdorferi patient isolat es as determined by cultivation differs from that assessed by PCR performed directly on patient tissue.