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The main  Borrelia  species causing Lyme borreliosis in Europe and Asia are  Borrelia afzelii ,  B .  garinii ,  B .  burgdorferi  and  B .  bavariensis . This is in contrast to the United States, where infections are exclusively caused by  B .  burgdorferi . Until to date the genome sequences of four  B .  afzelii  strains, of which only two include the numerous plasmids, are available. In order to further assess the genetic diversity of  B .  afzelii , the most common species in Europe, responsible for the large variety of clinical manifestations of Lyme borreliosis, we have determined the full genome sequence of the  B .  afzelii  strain K78, a clinical isolate from Austria. The K78 genome contains a linear chromosome (905,949 bp) and 13 plasmids (8 linear and 5 circular) together presenting 1,309 open reading frames of which 496 are located on plasmids. With the exception of lp28-8, all linear replicons in their full length including their telomeres have been sequenced. The comparison with the genomes of the four other  B .  afzelii  strains, ACA-1, PKo, HLJ01 and Tom3107, as well as the one of  B .  burgdorferi  strain B31, confirmed a high degree of conservation within the linear chromosome of  B .  afzelii , whereas plasmid encoded genes showed a much larger diversity. Since some plasmids present in  B .  burgdorferi  are missing in the  B .  afzelii  genomes, the corresponding virulence factors of  B .  burgdorferi  are found in  B .  afzelii  on other unrelated plasmids. In addition, we have identified a species specific region in the circular plasmid, cp26, which could be used for species determination. Different non-coding RNAs have been located on the  B .  afzelii  K78 genome, which have not previously been annotated in any of the published  Borrelia  genomes.

Complete Genome Sequence of Borrelia afzelii K78 and Comparative Genome Analysis