Direct culturing is the standard assay for analysis of biological agents in water supplies, except for Cryptosporidium, which cannot be grown. The time required for organisms to grow on culture media limits this usefulness of this method when an agency must respond quickly to a crisis. The recent progress in developing genomic sequence databases has led to the development of a number of molecular methods that are capable of more rapid, highly-specific analyses. These assays use biomole-cules, such as DNA or proteins, as recognition elements based on compounds distinct for each pathogenic microorganism. Because every organism has unique biomarkers, tests have been developed for unequivocal identification of both waterborne pathogens and select agents. Knowledge of these bio-markers enables their combination with sensor schemes or detection methods. Although a number of these methods are useful in identification, issues remain concerning the ability of these methods to determine the viability of the pathogens present. Accordingly, these methods provide a "presumptive positive'' result, but organism culturing is still often required for a definitive answer. The determination of viability is important, especially for ascertaining whether the normal water treatment process is capable of eliminating the threat. Broad reviews of pathogen detection methods have been published (Epstein et al., 2002a; Straub and Chandler, 2003; Cirino et al., 2004), and although detailed description is beyond the scope of this chapter, a few methods will be noted below.
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