Genetic exchange and plasmid transfers in Borrelia burgdorferi sensu stricto revealed by three-way genome comparisons and multilocus sequence typing

Abstract

Comparative genomics of closely related bacterial isolates is a powerful method for uncovering virulence and other important genome elements. We determined draft sequences (8-fold coverage) of the genomes of strains JD1 and N40 of Borrelia burgdorferi sensu stricto, the causative agent of Lyme disease, and we compared the predicted genes from the two genomes with those from the previously sequenced B31 genome. The three genomes are closely related and are evolutionarily approximately equidistant (Ϸ0.5% pairwise nucleotide differences on the main chromosome). We used a Poisson model of nucleotide substitution to screen for genes with elevated levels of nucleotide polymorphisms. The three-way genome comparison allowed distinction between polymorphisms introduced by mutations and those introduced by recombination using the method of phylogenetic partitioning. Tests for recombination suggested that patches of high-density nucleotide polymorphisms on the chromosome and plasmids arise by DNA exchange. The role of recombination as the main mechanism driving B. burgdorferi diversification was confirmed by multilocus sequence typing of 18 clinical isolates at 18 polymorphic loci. A strong linkage between the multilocus sequence genotypes and the major alleles of outer-surface protein C (ospC) suggested that balancing selection at ospC is a dominant force maintaining B. burgdorferi diversity in local populations. We conclude that B. burgdorferi undergoes genome-wide genetic exchange, including plasmid transfers, and previous reports of its clonality are artifacts from the use of geographically and ecological isolated samples. Frequent recombination implies a potential for rapid adaptive evolution and a possible polygenic basis of B. burgdorferi pathogenicity.omparative genomics of closely related species is a powerful method for tracking microbial epidemics (1, 2), uncovering microbial virulence factors (3-5), and annotating genes and other conserved elements in genomes (6, 7). A powerful method of bacterial genotyping is multilocus sequence typing (MLST), which is the comparative sequencing of selected genes (5,(8)(9)(10). (Note that in this article by MLST we refer to the comparative sequencing of multiple loci at large, not necessarily housekeeping genes.) We have taken a comparative genomics approach to identify polymorphic ORFs in the genomes of Borrelia burgdorferi sensu stricto, which is the predominant bacterial species causing Lyme disease in North America (11). Measuring rates of sequence evolution and selective constraints (12, 13) is a means of uncovering virulence factors and candidates for vaccine, diagnostics, and therapeutics.Early population studies of B. burgdorferi using multilocus enzyme electrophoresis (MLEE) (14) and DNA sequences (15) found little evidence for genetic exchange among different isolates. In fact, one report (16) concluded that B. burgdorferi was among the most clonal of bacterial species. However, these studies were based on archival strains isolated from several worldwide locations, ...

The genetic structure of Borrelia afzelii varies with geographic but not ecological sampling scale

“…It has been proposed that not only the geographic but also the ecological scale of sampling could affect the observed genetic structure of pathogens in general and Borrelia in particular (Frank, 2002;Qiu et al, 2004). This view is supported by the finding of significant host specificity in B. burgdorferi ss, where different ospC genotypes were associated with different mammal species (Brisson & Dykhuizen, 2004).…”

“…Taken together, the present and previous studies (Bunikis et al, 2004;Qiu et al, 2004;Attie et al, 2007) show that even though Borrelia sp. seems to be capable of genome-wide recombination, the genetic structure is to a large extent clonal as a result of epidemic spread of certain haplotypes.…”

“…Several studies have found strong linkage between ospC and other loci on other plasmids as well as on the chromosome, showing that B. burgdorferi ss is highly clonal (Dykhuizen & Baranton, 2001;Qiu et al, 2004;Attie et al, 2007;Hanincova et al, 2008;Margos et al, 2008). However, there is also strong evidence that recombination occurs.…”

“…First, the ospC gene has been found to evolve mainly through intragenic recombination rather than point mutation (Dykhuizen & Baranton, 2001). Second, by comparing the patterns of polymorphism across the genomes of three different isolates of B. burgdorferi ss, Qiu et al (2004) concluded that recombination is not restricted to ospC, but that B. burgdorferi ss indeed undergoes genome-wide exchange of larger pieces of DNA. They suggested that the high degree of clonality often observed might be a result of sampling across geographically separated and differentiated populations.…”

Molecular Evolution of Pathogenicity-Island Genes in Pseudomonas viridiflava

“…Like Arabidopsis R genes, however, the Phyophthora infestans scr74 gene family of effectors may be subject to diversifying selection (Liu et al 2005). Limited evidence of balancing selection acting upon virulence-related genes is found in Fusarium graminearum (Ward et al 2002) and in Borrelia burgdorferi (Qiu et al 2004). A comprehensive survey of Pseudomonas syringae effectors identified an additional seven gene families with domains subject to diversifying selection, although the majority of gene families were shaped by purifying selection (Rohmer et al 2004).…”