Current Limitations on the Use of DNA Microarrays in Diagnostics in Medical Microbiological Laboratories

Currently, the limitation on a broader application of pathogenomic tools (DNA microarrays) in microbial diagnostics basically relates to costs and operative overheads. Upfront investment and molecular expertise are required for the development and validation of in-house genetic techniques and may hinder application in smaller laboratories. Aside from their costs and the difficulties associated with designing and making a suitable array, the most obvious problems are those of quality control, because of the difficulties of standardization and reproducibility associated with the large number of probes on an array, and the large number of slides that need to be made. Commercially available arrays may be inflexible because they are based on just one target sequence, whereas in-house arrays of oligonucleotides or PCR amplicons spotted on glass slides may be contaminated if PCR amplicons are used. Additionally, a number of relevant experimental factors must be considered in order to obtain satisfactory research results. Sample preparation and processing are crucial, and researchers must pay careful attention to RNA isolation, target amplification, target labeling, hybridization, detection, data processing, and data analysis. Further commercialization will certainly improve the user-friendliness of these techniques, increase their use, and make microarray technology more affordable. As microbial evolution continues, the composition of microarrays has to be continuously adapted to the current pattern of microbial virulence factors and antibiotic resistance genes.

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