Unravelling the genomic landscape of Canadian <i>Borrelia burgdorferi</i>: a comparison across global strains

The main agent of Lyme borreliosis (LB) in North America, the bacteria <i>Borrelia burgdorferi</i>, is spreading in Canada following the northward expansion of its primary tick vectors, <i>Ixodes scapularis</i> and <i>Ixodes pacificus</i>. Despite the importance of this pathogen for human health, the precise geographical origin and genome structure of Canadian <i>B. burgdorferi</i> strains remain to be determined, and no complete genome sequence from this region is available. The complex genome structure of <i>Borrelia</i> species makes their assembly challenging, but the latest long-read sequencing technologies and bioinformatics software now enable <i>de novo</i> assembly of <i>Borrelia</i> genomes with high efficacy. In this study, we sequenced and assembled the genomes of six Canadian <i>B. burgdorferi</i> strains to compare their content and structure to additional <i>Borrelia</i> genomes from the USA and Europe. We successfully reconstructed the genome, comprising chromosomes and plasmids of the six Canadian strains. These genomes showed an overall similar structure compared to other <i>B. burgdorferi</i> strains. Phylogenetic inferences highlighted topological differences in the placement of <i>B. burgdorferi</i> strains between the chromosome and the cp26 and lp54 plasmids. Synteny analyses revealed important replicon sequence conservation across strains while highlighting a high proportion of shared gene sequences among the replicons of the same strain, especially for cp32 plasmids. We describe the first complete genomes of Canadian <i>B. burgdorferi</i> strains and present a strategy for the assembly, annotation, comparative analysis of plasmids and their evolution in the same bacterial genus. While the genome content and structure of Canadian strains are similar to other <i>B. burgdorferi</i> strains, the information in the plasmids and genes they harbour will be useful to elucidate the origins and evolution of LB in Canada.