Genetic landscape of Borrelia burgdorferi sensu stricto in Canada: a study of genetic diversity.

Borrelia burgdorferi sensu stricto (s.s.), the causative agent of Lyme disease in North America, exhibits considerable genetic diversity. In order to gauge rates of recombination and the degree of geographically structuring within the population we carried out a comprehensive whole-genome comparison of B. burgdorferi s.s. strains (n = 64) across three Canadian regions - Nova Scotia (NS), Ontario (ON), and Manitoba (MB). Using a multi-marker approach (MLST, ospC, RSP, RST, IGS), we identified 12 genetically coherent groups that were stable across both core and accessory genome phylogenies. Our analyses reveal a clear geographic gradient of clonality, with NS harboring highly clonal and modular populations (clonal ratio = 4, modularity Q = 0.68), while ON/MB strains exhibited more recombination, shared markers, and genetic connectivity. Genes like ospC showed high recombination rates (R/θ = 4.25), whereas others (ospA, P45-13) evolved primarily via mutation (R/θ < 0.10), illustrating distinct selective pressures in host versus vector environments. Despite these differences, lineages remained phylogenetically robust across markers. These findings highlight how evolutionary processes shape the structure and diversity of B. burgdorferi s.s. populations in Canada and provide insights into its geographic spread and population ecology.