Tools for the Population Genomics of the Tubercle Bacilli

Advances in sequencing technology have resulted in a rapidly increasing number of completed bacterial genome sequences (http://www.tigr.org/tdb/mdb/mdbcomplete.html,http://igweb.integratedgenomics.com/GOLD/). The relatively small size and limited gene content of these bacterial genomes make them readily amenable to functional genomic analysis. DNA microarrays in particular are proving practical and affordable tools for groups to study the global gene expression of particular organisms (Wilson et al. 1999). Most of the published studies using bacterial genome microarrays have used them to study alterations in gene expression caused by a targeted mutation of a specific regulatory gene or following an external stimulus. However, DNA microarrays also provide a means for complete genome comparisons, either between individual strains from the same species or between closely related species.

In essence, genomic DNA from the bacterial strain of interest is hybridized to the DNA microarray representing the entire genome of the sequenced reference strain and analyzed to determine if any genomic regions of the hybridizing strain are absent relative to the reference strain (Behr et al. 1999). These ‘deleted’ regions are then further analyzed by PCR and sequencing to define precisely the limits of any apparently deleted region. This currently underexploited use of microarrays will allow researchers to rapidly carry out whole-genome comparisons of large numbers of bacterial strains to determine intra- and interspecies genome variation. Such an analysis has the potential to provide important insights into bacterial evolution, horizontal gene transfer, speciation, and in the case of pathogenic bacteria, the genetic basis of interstrain variations of virulence.

This type of whole-genome deletion detection has already been successfully applied to members of the Mycobacterium tuberculosis complex, a single species as defined by DNA/DNA hybridization studies (Imaeda 1985). The M. tuberculosiscomplex includes M. tuberculosis, the causative agent in the vast majority of human tuberculosis cases, M. microti …