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Background  Lyme disease is a global public health problem caused by the spirochaete  Borrelia burgdorferi . Our previous studies found differences in disease severity between  B. burgdorferi  B31- and  B. garinii  SZ-infected mice. We hypothesized that genes that are differentially expressed between  Borrelia  isolates encode bacterial factors that contribute to disease diversity.    Methods  The present study used high-throughput sequencing technology to characterize and compare the transcriptional profiles of  B. burgdorferi  B31 and  B. garinii  SZ cultured  in vitro . Real-time quantitative RT-PCR was used to validate selected data from RNA-seq experiments.    Results  A total of 731 genes were differentially expressed between  B. burgdorferi  B31 and  B. garinii  SZ isolates, including those encoding lipoproteins and purine transport proteins. The fold difference in expression for  B. garinii  SZ versus  B. burgdorferi  B31 ranged from 22.07 to 1.01. Expression of the  OspA ,  OspB  and  DbpB  genes were significantly lower in  B. garinii  SZ compared to  B. burgdorferi  B31.    Conclusions  The results support the hypothesis that global changes in gene expression underlie differences in  Borrelia  pathogenicity. The findings also provide an empirical basis for studying the mechanism of action of specific genes as well as their potential usefulness for the diagnosis and management of Lyme disease.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-014-0623-2) contains supplementary material, which is available to authorized users.

RNA-Seq-based analysis of changes in Borrelia burgdorferi gene expression linked to pathogenicity