Microarrays are analytical tools developed over the past decade that enable high-throughput multiplexed pathogen analysis. Microarray platforms employ thousands of gridded, microscopic DNA spots that are used, in parallel, to interrogate a sample, essentially screening the sample against an immobilized library of pathogen-specific DNA sequences. Real-time PCR is capable of detection of a few DNA target sequences; microarrays can address hundreds to thousands of target DNA sequences simultaneously. Conversely, although real-time PCR has been shown to detect a single copy, or only a few copies, of DNA, microarrays are generally less sensitive. Microarrays have now been developed to interrogate a broad spectrum of pathogens, including a range of food and water microbial pathogens (Chizhikov et al., 2001; Sergeev et al., 2004), as well as select agents (Wilson et al., 2002). As microar-ray platforms are becoming more specialized, some formats have exhibited the ability to detect DNA even when present in low abundance (Epstein et al., 2002b) and have demonstrated the ability to rapidly subtype pathogen species (Borucki et al., 2004; Shepard et al., 2005). If these methodologies are developed further, comprehensive microarray formats will eventually be able to discriminate and identify the entire spectrum of microbial species, down to the subtype level, and will be of enormous value for the analysis of emerging pathogens.

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