Comparative Population Genomics of the Borrelia burgdorferi Species Complex Reveals High Degree of Genetic Isolation among Species and Underscores Benefits and Constraints to Studying Intra-Specific Epidemiological Processes

Type Article
Date 2014-04
Language English
Author(s) Jacquot MaudeORCID1, Gonnet Mathieu1, Ferquel Elisabeth2, Abrial David1, Claude Alexandre1, Gasqui Patrick1, Choumet Valerie2, Charras-Garrido Myriam1, Garnier Martine2, Faure Benjamin1, Sertour Natacha2, Dorr Nelly1, De Goer Jocelyn1, Vourc'h Gwenael1, Bailly XavierORCID1
Affiliation(s) 1 : INRA, Epidemiol Anim UR346, F-63122 St Genes Champanelle, France.
2 : Inst Pasteur, CNR Borrelia, Paris, France.
Source Plos One (1932-6203) (Public Library Science), 2014-04 , Vol. 9 , N. 4 , P. e94384 (19p.)
DOI 10.1371/journal.pone.0094384
WOS© Times Cited 17
Abstract

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 MB Open access
Figure S1. Mean likelihood values of Structure runs 665 KB Open access
Figure S2. Genetic differentiation between isolates from Munster and Guebwiller for B. burgdorferi s.s. and B. garinii. 2 MB Open access
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 MB Open access
Figure S4. Posterior distributions of parameters of the coalescent model M3. 714 KB Open access
Table S1. Description of the 63 strains of the B. burgdorferi species complex that were isolated and sequenced in this study 48 KB Open access
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 KB Open access
Table S3. Description of the 23 sequenced strains isolated and sequenced in previous studies and used as references in this study. 45 KB Open access
Table S4. Bayes factors for each pair of coalescent models 15 KB Open access
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How to cite 

Jacquot Maude, Gonnet Mathieu, Ferquel Elisabeth, Abrial David, Claude Alexandre, Gasqui Patrick, Choumet Valerie, Charras-Garrido Myriam, Garnier Martine, Faure Benjamin, Sertour Natacha, Dorr Nelly, De Goer Jocelyn, Vourc'h Gwenael, Bailly Xavier (2014). Comparative Population Genomics of the Borrelia burgdorferi Species Complex Reveals High Degree of Genetic Isolation among Species and Underscores Benefits and Constraints to Studying Intra-Specific Epidemiological Processes. Plos One, 9(4), e94384 (19p.). Publisher's official version : https://doi.org/10.1371/journal.pone.0094384 , Open Access version : https://archimer.ifremer.fr/doc/00667/77887/