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Involvement of the nervous system in Lyme borreliosis may occur with or without erythema migrans and it may present with a variety of neurological symptoms. In this study we analysed phenotypic and genotypic characteristics of 40 Borrelia strains isolated from cerebrospinal fluid (CSF) of 38 Slovenian patients with different clinical manifestations of Lyme borreliosis. In seven of the patients, Borreliae were also isolated from skin lesions. Species identification and plasmid profiles were determined by pulsed-field gel electrophoresis and protein profiles by SDS-PAGE. MluI digestion profiles of Borrelia burgdorferi sensu lato DNA showed that 25 (62.5%) isolates were B. garinii, 14 (35%) B. afzelii, and one (2.5%) B. burgdorferi sensu stricto. All strains, except one, possessed a large plasmid and a varying number of smaller plasmids. Three (7.5%) isolates exhibited an unusual plasmid profile, with a large plasmid dimer or three copies of the large plasmid. In protein analyses, all strains expressed OspA protein. OspB was present significantly more often in B. afzelii than B. garinii strains (p=0.0000), while OspC was more often present in B. garinii than B. afzelii strains (p=0.0052). In the seven patients with Borreliae isolated also from the skin, the CSF and skin isolates were identical, either B. garinii (six patients) or B. afzelii (one patient). Species and plasmid heterogeneity as well as antigen diversity could play a role in the pathogenesis of the infection. When combined with our own earlier data, the results suggest species-related organotropism.