The Borrelia genome is composed of a linear chromosome and a number of variable circular and linear plasmids. Atypically large linear plasmids of 92 to 105 kb have been identified in several Borrelia burgdorferi sensu lato isolates and characterized. These plasmids carry the p27 and ospAB genes, which in other isolates reside on a 50-kb plasmid. Here we demonstrate that these plasmids are dimers of the 50-kb ospAB plasmid (pAB50). The 94-kb plasmid from isolate VS116, pVS94, was an exception and did not hybridize with any plasmid gene probes. When this plasmid was used as a probe, homologous sequences in other isolates were not detected, suggesting that it is unique to isolate VS116. These analyses provide insight into the mechanism of linear plasmid replication and the mechanisms by which plasmid variability can arise.Lyme disease, a tick-borne zoonosis (5,7,36,37), is caused by Borrelia burgdorferi, Borrelia garinii, and Borrelia afzelii (1,6,19,20,38). Related species of uncertain pathogenic potential, i.e., Borrelia japonica (18) and Borrelia andersonii (21), have also been identified. These five species are collectively referred to as B. burgdorferi sensu lato (BBsl). The BBsl genome is composed of variable linear and circular plasmids (15, 30) and a linear chromosome (11). The ospAB operon is carried on the largest of the linear plasmids, which ranges from 48 to 60 kb (31). We refer to this variably sized plasmid as the 50-kb ospAB plasmid or pAB50. The importance of the BBsl plasmids is underscored by the fact that they are present in all isolates and that they carry genes encoding metabolic enzymes (24). In view of this, the extent of plasmid variability among isolates is surprising. The significance of and the mechanisms involved in generating plasmid variability are not completely understood. Plasmid loss (32), recombination (17,22,28), and lateral transfer of plasmids among BBsl species (22) have been demonstrated to be contributing processes. Here we demonstrate that linear plasmid dimer formation also contributes to plasmid variability and discuss how these findings may provide information concerning the mechanisms of linear plasmid replication.Bacterial isolates analyzed in this study were cultivated at 34ЊC in BSK-H (Sigma) supplemented with 6% rabbit serum. Pulsed-field gel electrophoresis (PFGE) was performed to analyze plasmid content as previously described (21). Several isolates carrying 92-to 105-kb plasmids, 40 to 50 kb larger than those typically observed (2-4, 8, 16, 22, 31-35, 39), were identified (Table 1). Only B. burgdorferi R100 had been previously shown to carry a plasmid in this size range (26). Southern blot analyses with an ospA probe (ospA-5Ј-GGCTGCTAACATTT-TGCTTACATGC) revealed that the ospAB operon was carried by the large plasmids in IKA2, HO14 (Fig. 1), BO23, and R100 and by a 50-kb plasmid in VS116 (data not shown). In IKA2, a second plasmid of 47 kb also bound the probe (Fig. 1); however, after continued in vitro cultivation, this plasmid was lost and an ospAB-hybridizing ...