An Affymetrix Microarray Design for Microbial Genotyping
DEFENCE RESEARCH AND DEVELOPMENT SUFFIELD (ALBERTA)
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There is an ongoing requirement for development of high-density or multiplex assays for detection or identification of microbes. There is also a need to develop assays or toolsets that can detect or identify microbial threats without prior knowledge of the target microbes in a given sample. Indeed, some samples that contain no culturable material e.g. viable but non-culturable cells will nonetheless contain detectable DNA fragments which might be of value with respect to forensics or attribution of source. For many pathogenic microbes, various specific tests already exist, but there are few general methods wherein a single adaptable tool can be applied to multiple species or to previously uncharacterized organisms. The high-density DNA microarray has the potential to address many of these requirements and thus complements existing identification tools. The microarray platform has for example, the ability to detect microbial DNA that is not a perfect match to known genomic DNA sequences, thus making it possible to detect microbial variants that might otherwise be missed. In this report, the design and preliminary testing of a high-density DNA microarray for the purpose of microbial identification and detection is described.