Introduction to Pathogenomics

Abstract

This chapter provides an introduction to pathogenomics. Any bacterial genome-sequencing project comprises a number of steps and follows the 80:20 principle: that is, 80%, or more, of the work gets done in 20% of the time, while finishing the job consumes a disproportionate amount of effort. The first stage in any bacterial genome project is to choose one or more strains to sequence. The next stage in a genome-sequencing project is to grow enough bacterial cells to yield sufficient genomic DNA for the creation of a random shotgun library in Escherichia coli. Shotgun sequencing continues until an acceptable coverage of the genome has been achieved. The final stage in obtaining a bacterial genome sequence is finishing, during which all gaps are closed and all ambiguities resolved. A number of interesting features can be identified rapidly: repetitive sequences and homopolymeric tracts; noncoding RNA genes (tRNAs, rRNAs, small regulatory RNAs); recently acquired DNA; leading and lagging strands and the origin of replication. An interesting sideline will be the metagenomics of the bacteriophage community, given both the numerical preponderance of phages in the biosphere and their well-established role in the evolution and dissemination of bacterial virulence factors.