Modeling Bacterial Evolution with Comparative-Genome-Based Marker Systems: Application to Mycobacterium tuberculosis Evolution and Pathogenesis

Abstract

The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M. tuberculosis. Phylogenetic analysis using these "comparative-genome markers" (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. To investigate CGM-based phylogenies, we devised computer models to simulate sequence evolution and calculate new phylogenies based on an SNP format. We found that CGMs represent a distinct class of phylogenetic markers that depend critically on the genetic distances between compared "reference strains." Properly distanced reference strains generate CGMs that accurately depict evolutionary relationships, distorted only by branch collapse. Improperly distanced reference strains generate CGMs that distort and reroot outgroups. Applying this understanding to the CGM-based phylogeny of M. tuberculosis, we found evidence to suggest that this species is highly clonal without detectable lateral gene exchange. We noted indications of evolutionary bottlenecks, including one at the level of the PHRI "C" strain previously associated with particular virulence characteristics. Our evidence also suggests that loss of IS6110 to fewer than seven elements per genome is uncommon. Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure.

Genomic Comparison of PE and PPE Genes in the Mycobacterium avium Complex

“…These SNPs can be used for subspecies differentiation. SNPs are frequently used in epidemiological and evolutionary studies to differentiate between closely related species, subspecies, and strains of bacteria without knowledge of what effect the SNP may have on gene function or protein activity (1,19,24,27,47). …”

Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks

“…Comparison of multiple O157 genomes has shown that bacteriophage variation is a major factor in generating genomic diversity (25) and presumably underlies most genomic variability detected by PFGE (24,26). In contrast, the systematic analysis of SNPs, also useful for outbreak investigations, can resolve closely related bacterial genotypes, provide insights into the microevolutionary history of genome divergence (20,27), and contribute to an epidemiologic assessment of associations between bacterial genotypes and disease. Here we genotyped Ͼ500 clinical strains of EHEC O157 based on 96 SNPs that separated strains into genetically distinct groups and sequenced the genome of the O157 strain implicated in the spinach outbreak.…”

“…To assess the genetic diversity and variability in virulence among E. coli O157 strains, we developed a real-time PCR system for identifying synonymous and nonsynonymous mutations as SNPs (20)(21)(22)(23). Although molecular subtyping methods, such as pulsedfield gel electrophoresis (PFGE), reveal extensive genomic diversity among O157 outbreaks, ''DNA fingerprinting'' data are not amenable to population genetic or phylogenetic analyses.…”

Genomics: Anthrax and the art of war (against ascertainment bias)

“…The curious phenomenon of 'branch collapse' was originally identified in an elegant study on SNPs of Mycobacterium tuberculosis (Alland et al, 2003). Pearson et al extend this work and explicitly point out, using simulations, that only those mutational events falling on the evolutionary path between the two strains used to generate the panel of SNPs will be discovered.…”