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Lyme disease spirochete Borrelia burgdorferi expresses diverse subsurface yet antigenically cross-reactive Bdr protein paralogs from distinct circular- and linear-plasmid loci. We assessed the possible effects of in vitro and in vivo growth on bdr locus structure, searching for recombinational events leading to either deletions or insertions of central repeat units or novel amino- and carboxy-terminus combinations. Our data indicate that, apart from plasmid loss during in vitro cultivation, the bdr paralog loci of strain B31 are stable. This suggests that recombinatorial variation of bdr genes is not essential for persistent mammalian infection.