MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi

Abstract

Lyme borreliosis, caused by the tick-borne bacterium Borrelia burgdorferi, has become the most common vector-borne disease in North America over the last three decades. To understand the dynamics of the epizootic spread and to predict the evolutionary trajectories of B. burgdorferi, accurate information on the population structure and the evolutionary relationships of the pathogen is crucial. We, therefore, developed a multilocus sequence typing (MLST) scheme for B. burgdorferi based on eight chromosomal housekeeping genes. We validated the MLST scheme on B. burgdorferi specimens from North America and Europe, comprising both cultured isolates and infected ticks. These data were compared with sequences for the commonly used genetic markers rrs-rrlA intergenic spacer (IGS) and the gene encoding the outer surface protein C (ospC). The study demonstrates that the concatenated sequences of the housekeeping genes of B. burgdorferi provide highly resolved phylogenetic signals and that the housekeeping genes evolve differently compared with the IGS locus and ospC. Using sequence data, the study reveals that North American and European populations of B. burgdorferi correspond to genetically distinct populations. Importantly, the MLST data suggest that B. burgdorferi originated in Europe rather than in North America as proposed previously.

Fig. 1.

Bayesian phylogenetic inference of IGS sequences of B. burgdorferi. Posterior probability values of clades are provided. Symbols refer to the major IGS genotypes as defined by Bunikis et al. (41). Samples 21509LT and 22521LT were excluded because of the lack of PCR products. Non-color-coded strains are from the Northeast and Midwest United States. Yellow, strains from California; blue, strains from Europe. The branch length of the outgroup B. garinii is not according to scale (indicated by slashes). (Scale bar: 10% divergence.)

Fig. 2.

Bayesian phylogenetic inference of ospC gene sequences of B. burgdorferi. Posterior probability values of clades are provided. Symbols refer to the major IGS genotypes as defined by Bunikis et al. (41). Samples 21509LT, 22521LT, 20604LT, and 20111LT are missing because of the lack of PCR products. Non-color-coded strains are from the Northeast and Midwest United States. Yellow, strains from California; blue, strains from Europe. (Scale bar: 10% divergence.)

Fig. 3.

Bayesian phylogenetic inference of concatenated sequences of the housekeeping genes (clpA, clpX, nifS, pepX, pyrG, recG, rplB, and uvrA) of B. burgdorferi. Posterior probability values of clades are provided. Symbols refer to the major IGS genotypes as defined by Bunikis et al. (41). Non-color-coded strains are from the Northeast and Midwest United States. Yellow, strains from California; blue, strains from Europe. The branch length of the outgroup B. garinii is not according to scale (indicated by slashes). (Scale bar: 1% divergence.)