Genomics of Bacterial Pathogen Strain Variation

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SELECTBIO

Bacterial pathogens used to be represented in research by a limited number of model strains used in molecular genetics and animal challenge studies. Next-generation sequencing technologies are broadening our frame of reference to take in natural genome and transcriptome diversity. Our group has analyzed multiple genome sequences from a number of species, including Bacillus anthracis, Chlamydia trachomatis and Yersinia pestis to narrow down the genes that are unique to the pathogenic members of the group. These data can also be used for reconstructions of past bottlenecks and selective sweeps to help discover new pathogenic niche-adaptation functions. Another next-generation approach, RNA-Seq, was used for a genome-wide determination of anti-sense transcription in the pathogen B. anthracis and to ascertain variation in global mRNA decay rates at the single nucleotide level in closely-related non-pathogen strains. The challenge for the future will be integrate population genomics and transcription studies. There are opportunities to develop new tools to create better genome sequences and to address interesting but difficult problems such as using known genetic variations to predict the level of virulence of a given pathogen genome.