Microarrays have the unprecedented potential to simultaneously detect and identify thousands of microbial genes, which provides another evolutionary technical advance in the field of clinical microbiology. Although, historically, microarrays have been used largely for gene expression studies, microarrays have gradually been applied in the detection and characterization of microbial pathogens, determination of antimicrobial resistance, typing of microbial pathogens, and monitoring of microbial infections by investigating host genomic expression and polymorphism profiles. Even with these major advances, the potential power behind microarray applications in clinical microbiology has yet to be fully realized. The ability to detect multiple pathogens and/or monitor the variability of normal microbial populations in a disease process could transform our current understanding of infectious diseases. In addition, massively parallel sequencing performed by microarray analysis offers the opportunity of sequencing directly from complex clinical specimens. This metagenomics approach will allow a comprehensive analysis of every nucleic acid in the specimen. For these robust applications, high-density microarray platforms must be able to transition from translational research laboratories to the clinical laboratory. It is unlikely that traditional, planar microarrays will soon appear in clinical microbiology laboratories due to their high cost, relative lack of flexibility, and limited throughput. The ideal microarray platform for the diagnostic laboratory is a low- to medium-density array that offers limited, reliable, and straightforward results without the need for sophisticated equipment and data management (133
). Indeed, platforms that have begun to meet these criteria have been developed, such as electronic microarrays and suspension bead arrays.
With the potential power of microarray analysis comes abundant challenges, particularly in relation to the diagnostic laboratory. Several critical issues need to be resolved before microarray-based techniques can be widely implemented in clinical microbiology services. Due to the potential variability in multiple steps included in the microarray analysis, it is difficult to compare quantitative data between, and even within, microarray experiments. Substantial obstacles still exist along the entire spectrum of preanalytical-to-postanalytical analysis. Heterogeneous clinical specimens present unique challenges with respect to sensitivity, specificity, quantification, and data analysis of microarrays that are not encountered during the analysis of pure cultures. In addition, optimization of extraction, labeling, and hybridization; incorporation of appropriate quality controls, design, and implementation of clinical validation studies; and management and interpretation of data remain challenges in a clinical setting. Moreover, laboratories must account for microarray reproducibility in production and analysis, cost of implementation, acquisition of appropriately skilled laboratorians, as well as intellectual property and reimbursement issues. Compared to real-time PCR, microarray analysis requires additional manipulations including hybridization and washing, which increase the contamination risk and the amount of hands-on time needed, both steps backwards in diagnostic molecular microbiology.
Although improvements are still needed to make the majority of microarray applications amenable to clinical microbiology laboratories, the future role of these robust technologies in diagnostic microbiology is indisputable. Microarray-based analyses will revolutionize infectious disease diagnostics through the detection and identification of previously unknown or unsuspected pathogens, by transforming our current view of multiplexed laboratory testing, and by expanding pathogen detection to include bacterial population-based analyses and host-specific responses (135
). As more pathogen genomes and targeted genes are sequenced, costs associated with microarray production decrease, and FDA-cleared products become available, diagnostic applications of microarray-based analyses will continue to expand. As PCR has done in the last 25 years, and more recently real-time PCR, microarray technology will undoubtedly transform the diagnostic capabilities of clinical laboratories, ushering us into a new molecular revolution.