Design of Genomic Signatures for Pathogen Identification and Characterization

This chapter addresses issues associated with the identification of signatures based on genomic DNA/RNA, which can be used to identify and characterize pathogens for biodefense and microbial forensic goals. Genomic signature-based identification techniques have the advantage of being precise, highly sensitive, and relatively fast in comparison to biochemical typing methods and protein signatures. Classic biochemical typing methods were developed long before knowledge of DNA and resulted in dozens of tests that are used to roughly characterize the major known pathogens. Genomic signatures can be intended for many different purposes and applied at multiple different resolutions. Organism signatures are intended to uniquely identify the organisms involved. Mechanism signatures can be best thought of as identifying particular genes that result in functional properties such as virulence, antibiotic resistance, or host range. The primary reason to identify mechanisms, independent of organisms, is to detect potential genetic engineering. A secondary reason is that nature has shared many important mechanisms on its own over the millennia, and thus they may not be sufficiently unique to identify specific organisms. Method signatures present yet another dimension of analyzing pathogens: evidence of potential bacterial genetic engineering may be seen in a genome by checking for traces of the bacterial vectors that may have been used to insert one or more foreign genes and related components into the genome being modified.