Solid‐ and Liquid‐Phase Array Technologies

This chapter focuses on DNA-based hybridization array technology. The chapter reviews the methodologies of cDNA, oligonucleotide, electronic, and liquid bead arrays. In each of these methodologies, the probe refers to the DNA sequence bound to the solid surface support in the microarray, whereas the target is the “unknown” sequence of interest. Printed microarrays have the advantages of simplicity and relatively low cost compared to synthesized microarrays, which are discussed in the chapter. While two-dimensional microarrays have had an impact on our understanding of the microbial world and the application of this diagnostic potential to infectious diseases, the most widespread and practical application is the use of liquid bead suspension arrays in diagnostic microbiology, which is therefore emphasized when applicable. The potential use of low- or medium-density arrays for the simultaneous detection of large numbers of microbial genetic targets is one of the most promising areas in applying microarray technology to diagnostic microbiology. Broad-range amplification often focuses on the rRNA genes (16S, 18S, 23S, or intergenic transcribed spacers) due to the inherent dichotomy of conserved and polymorphic sequences. Though the range of organisms included was relatively limited (species of Bacillus , Listeria , Staphylococcus , Escherichia , Shigella , Klebsiella , Salmonella , Enterobacter , Ralstonia , Burkholderia , and Pseudomonas ), this study provides proof of principle for the use of suspension arrays for the identification of broad-range amplification products. Though broad-range amplification typically focuses on the rRNA genes, other targets have been employed.