DOI 10.1371/journal.pone.0094384 Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals and birds. These features make the Borrelia burgdorferi species complex an attractive biological model that can be used to study the diversification and the epidemiology of endemic bacterial pathogens. We investigated the potential of population genomic approaches to study these processes. Sixty-three strains belonging to three species within the Borrelia burgdorferi complex were isolated from questing ticks in Alsace (France), a region where Lyme disease is highly endemic. We first aimed to characterize the degree of genetic isolation among the species sampled. Phylogenetic and coalescent-based analyses revealed clear delineations: there was a similar to 50 fold difference between intra-specific and inter-specific recombination rates. We then investigated whether the population genomic data contained information of epidemiological relevance. In phylogenies inferred using most of the genome, conspecific strains did not cluster in clades. These results raise questions about the relevance of different strategies when investigating pathogen epidemiology. For instance, here, both classical analytic approaches and phylodynamic simulations suggested that population sizes and migration rates were higher in B. garinii populations, which are normally associated with birds, than in B. burgdorferi s.s. populations. The phylogenetic analyses of the infection-related ospC gene and its flanking region provided additional support for this finding. Traces of recombination among the B. burgdorferi s. s. lineages and lineages associated with small mammals were found, suggesting that they shared the same hosts. Altogether, these results provide baseline evidence that can be used to formulate hypotheses regarding the host range of B. burgdorferi lineages based on population genomic data.
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Publisher's official version | 19 | 1 Mo | ||
Figure S1. Mean likelihood values of Structure runs | - | 665 Ko | ||
Figure S2. Genetic differentiation between isolates from Munster and Guebwiller for B. burgdorferi s.s. and B. garinii. | - | 2 Mo | ||
Figure S3. Distribution of Tajima's D values obtained from contiguous 1-kb windows for the three species of Borrelia included in this study. | - | 2 Mo | ||
Figure S4. Posterior distributions of parameters of the coalescent model M3. | - | 714 Ko | ||
Table S1. Description of the 63 strains of the B. burgdorferi species complex that were isolated and sequenced in this study | - | 48 Ko | ||
Table S2. Percentage of the length of reference sequences onto which raw sequences were mapped for each strain of the B. burgdorferi species complex examined in this study. | - | 68 Ko | ||
Table S3. Description of the 23 sequenced strains isolated and sequenced in previous studies and used as references in this study. | - | 45 Ko | ||
Table S4. Bayes factors for each pair of coalescent models | - | 15 Ko |
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