Utilisation des outils phylogéographiques pour explorer la diversité génétique de Borrelia burgdorferi et le paysage génétique de la maladie de Lyme au Canada

Lyme borreliosis is the most reported zoonotic infectious disease in temperate zones with significant consequences for human health. In Canada, it is considered to be emerging due to the expansion of the Ixodes scapularis tick vector to new areas in southern Canada where it has become established. Therefore, endemic areas of Lyme disease continue to grow, and are being promoted by climate change. These events coincide with adaptive radiation of B. burgdorferi in North America.  Within this problem, the phylogeographic pictures of the pathogen and its vector show surprisingly little correlation despite their intimate ecological association. The environmental risk assessment of Lyme disease requires a clear comprehension of the different patterns acting and driving the expansion of the pathogen and its vector. This picture is made more complex by considering the genetic diversity of B. burgdorferi which is important to its probable effects on diagnostic test performance and the differential pathogenicity amongst strains.  Some answers to these problems may be found by study of the bacterial genetics of this pathogen to improve knowledge of its relationship with its vector and hosts.  In this study we investigated the diversity and the genetic structure of B. burgdorferi sensu stricto populations in southern Canada and northern US by using phylogeographic tools: i) phylogenetic methods to explore the historical and the evolutionary processes of B. burgdorferi and ii) geo-spatial modeling to define the spatial distribution of different strains and their patterns of spread.  A total of 750 samples of B. burgdorferi (477 samples are from US and Canada which are available in the pubmlst.org/bburgdorferi/, and 273 samples collected using active surveillance in Canada and analyzed for the first time in this study) were used to reconstruct the phylogenetic relationship between different strains genotyped using MLST approach. Two other complementary approaches were used to strain-type B. burgdorferi, the outer surface protein C (ospC) and the ribosomal spacer rrs-rrlA (IGS).  It was found that the genetic diversity of B. burgdorferi in Canada is relatively similar to that of the US but only 1/5 strains are common to the both countries. This shows that the phylogeographic image of B. burgdorferi in North America appears to be more complex than previously known: i) geographic complexity because strains of various geographical origins form significant clades and others which have the same geographical origin but are genetically more distant dispersed on different clades (this is a probable signal of refugial populations) and ii) a genetic complexity since 90% of genetic exchanges occur within closely related phylogenetic groups. Such genetic structure can be driven by an ecological process, and we hypothesized that the associations of B. burgdorferi genotypes with specific hosts reduced gene flow between different groups. Statistical modeling allowed the identification of different associations between genotypes and certain rodent host species: CC34 and ospC G with Eastern Chipmunk; CC403, ospC A and RST1 with the white-footed mice; and CC4, ospC H and IGS 2D with the deer mice.  However, the phylogeny also showed that strains associated with chipmunk are older relatively to those associated with mice, which appear to have evolved more recently.  Studies based on the chipmunk fossil data in North America corroborate this hypothesis. In fact, this species was one of the few small mammals that survived during the glacial-interglacial periods which thought allowed the B. burgdorferi surviving. It had undergone a southward migration, whereas mice known to be more sensitive to climatic conditions had experienced a Northward migration after the last Pleistocene which led all these small mammals to share a common history. Therefore, host adaptations may have shaped the contemporary phylogeography of the pathogen in North America, which may be the driving force behind the differential pathogenicity of B. burgdorferi genotypes. Geo-spatial modeling using conditional probabilities showed that rodent-associated strains (e.g. ST1 of CC403 that is associated with white-footed mice) exhibit specific patterns of occurrence of dispersal driven by the landscape characteristics of forest connectivity. This study provides i) a first comprehensive phylogeographic picture of B. burgdorferi in southern Canada that is essential to understand the evolutionary epidemiology of Lyme disease in Northern America, ii) knowledge of the high genetic diversity in Canada that may be key to understanding geographic variations in occurrence of pathogenic strains and improving the specificity and sensitivity of diagnostic tests, and iii) understanding the methods of dispersion of B. burgdorferi in Northern America. Together these findings will improve our ability to predict risk from Lyme disease in Canada, and will drive research into new diagnostic methods.

Keyphrases: typage multi-locus, Lyme disease, Phylogeography, Evolutionary history, Multi-locus typing, Landscape connectivity, Spatial modeling