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Background  Lyme disease, caused by various species of  Borrelia , is transmitted by  Ixodes  ticks in North America and Europe. Studies have shown the genotype of  Borrelia burgdorferi  sensu stricto (s.s.) or the species of  B. burgdorferi  sensu lato (s.l.) affects the ability of the bacteria to cause local or disseminated infection in humans.    Methodology/Principal Findings  We used a multilocus PCR electrospray mass spectrometry assay to determine the species and genotype  Borrelia  from ticks collected in New York, Connecticut, Indiana, Southern Germany, and California and characterized isolates from parts of the United States and Europe. These analyses identified 53 distinct genotypes of  B. burgdorferi  sensu stricto with higher resolution than ospC typing. Genotypes of other members of the  B. burgdorferi  sensu lato complex were also identified and genotyped including  B. afzelii, B. garinii, B. lusitaniae, B. spielmanii, and B. valaisiana . While each site in North America had genotypes unique to that location, we found genotypes shared between individual regions and two genotypes found across the United States. Significant  B. burgdorferi  s.s. genotypic diversity was observed between North America and Europe: only 6.6% of US genotypes (3 of 45) were found in Europe and 27% of the European genotypes (3 of 11) were observed in the US. Interestingly, 39% of adult  Ixodes scapularis  ticks from North America were infected with more than one genotype of  B. burgdorferi  s.s. and 22.2% of  Ixodes ricinus  ticks from Germany were infected with more than one genotype of  B. burgdorferi  s.l.    Conclusions/Significance  The presence of multiple  Borrelia  genotypes in ticks increases the probability that a person will be infected with more than one genotype of  B. burgdorferi , potentially increasing the risks of disseminated Lyme disease. Our study indicates that the genotypic diversity of  Borrelia  in ticks in both North America and Europe is higher then previously reported and can have potential clinical consequences.

Genotypic Variation and Mixtures of Lyme Borrelia in Ixodes Ticks from North America and Europe