Detection/identification of microbes using microarrays


  1. Ruttan, C.C.
  2. Mah, D.C.W.
Corporate Authors
Defence R&D Canada - Suffield, Ralston ALTA (CAN);Canada West Biosciences Inc, Camrose Alta (CAN)
Microarray technology provides the potential for rapid identification of an unknown pathogen in a single test. In order to explore the utility of this tool, a custom Affymetrix DNA microarray chip was designed to recognize a wide variety of bacteria to the species and strain level. Antigenomic probes were included on the lower portion of the chip to investigate the potential of rapid visual assessment of organisms’ footprints. Since pre-existing protocols and analysis software were unavailable for this work, protocols were optimized and a variety of data analysis options were investigated. Experiments were conducted on a number of pure DNA samples and mixed samples with equal quantities of input DNA. The effect of DNA amplification and sample dilution on signal intensity was also investigated. The chips were readily able to identify the correct pathogen from pure samples but signal levels dropped with decreased input DNA. Amplified mixed DNA, both pre-amplification and post-amplification sample mixtures, produced different results from mixed unamplified DNA requiring more complex analysis technique or a better balancing of the number of probes designed for each organism. The dilution series demonstrated that signal intensity reduction corresponds to the decrease in template DNA (i.e. 1/10 DNA has 1/10 signal intensity). In all, 3,119 probes were selected that are strongly specific and sensitive for the organisms tested and these provide an excellent basis for future work wi

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Report Number
DRDC-SUFFIELD-CR-2012-018 — Contractor Report
Date of publication
01 Jul 2012
Number of Pages
Electronic Document(PDF)

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