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Background  Lyme disease in the United States is caused primarily by  B. burgdorferi  sensu stricto while other species are also prevalent in Europe. Genetic techniques have identified several chromosomal and plasmid-borne regulatory and virulence factors involved in Lyme pathogenesis. B31 and N40 are two widely studied strains of  B. burgdorferi,  which belong to two different 16 S-23 S  r RNA  s pacer  t ypes (RST) and outer surface protein C (OspC) allelic groups. However, the presence of several known virulence factors in N40 has not been investigated. This is the first comprehensive study that compared these two strains both  in vitro  and using the mouse model of infection.    Results  Phylogenetic analyses predict B31 to be more infectious. However, our studies here indicate that N40D10/E9 is more infectious than the B31 strain at lower doses of inoculation in the susceptible C3H mice. Based-upon a careful analyses of known adhesins of these strains, it is predicted that the absence of a known fibronectin-glycosaminoglycan binding adhesin,  bbk32 , in the N40 strain could at least partially be responsible for reduction in its binding to Vero cells  in vitro . Nevertheless, this difference does not affect the infectivity of N40D10/E9 strain. The genes encoding known regulatory and virulence factors critical for pathogenesis were detected in both strains. Differences in the protein profiles of these  B. burgdorferi  strains  in vitro  suggest that the novel, differentially expressed molecules may affect infectivity of  B. burgdorferi . Further exacerbation of these molecular differences  in vivo  could affect the pathogenesis of spirochete strains.    Conclusion  Based upon the studies here, it can be predicted that N40D10/E9 disseminated infection at lower doses may be enhanced by its lower binding to epithelial cells at the site of inoculation due to the absence of BBK32. We suggest that complete molecular analyses of virulence factors followed by their evaluation using the mouse infection model should form the basis of determining infectivity and pathogenicity of different strains rather than simple phylogenetic group analyses. This study further emphasizes a need to investigate multiple invasive strains of  B. burgdorferi  to fully appreciate the pathogenic mechanisms that contribute to Lyme disease manifestations.

Comparative molecular analyses of Borrelia burgdorferi sensu stricto strains B31 and N40D10/E9 and determination of their pathogenicity