Bacterial epidemiology and biology--lessons from genome sequencing

Abstract

Next-generation sequencing has ushered in a new era of microbial genomics, enabling the detailed historical and geographical tracing of bacteria. This is helping to shape our understanding of bacterial evolution.

Figure 1

Phyogeography of Yersinia pestis, identifying transmission routes out of China and single introductions into the US and Madagascar [4]. The figure represents a minimal spanning tree describing the relationship of the Y. pestis isolates. Colored circles represent genotypes, colored according to geographical location, and the size of the circle indicates the number of strains with that genotype. Letters within the circles indicate node designations. Grey text on lines between nodes shows the numbers of SNPs separating each node, except that one or two SNPs are indicated by thick and thin black lines, respectively. It is clear that the different genotypes show a strong geographical signal, and the relationships between them therefore suggest geographical transmission routes.

Figure 2

Changes in Group A Streptococcus subclones within three epidemics over time. The frequency distribution of all strains in the three epidemics is shown in grey, with three peaks of infection centered around 1995, 2000, and 2005. Ten major subclones (SC1 to SC10) were identified among the 344 strains collected between 1992 and 2007. The widths of the colored SC symbols show the temporal distribution of the SCs, and the heights are proportional to the annual abundance. Arrows between SCs indicate estimated relationships and give differences in the loci assessed [7]. It can be seen that although there is some carry-over of lineages between epidemic peaks, new lineages arise and contribute to each epidemic.