S23SrDNA Arrays

Microarrays offer tremendous potential for microbial community analysis, pathogen detection, and process monitoring in both basic and applied environmental science. In the hybridization fingerprinting approaches, the sensitivity of PCR and the specificity of oligonucleotide microarray hybridization are combined to enable microbial identification through analysis of the 5' region of prokaryotic 16S-rRNA genes of different bacterial strains. Special attention is paid to the impact of molecular tools and applications on the diagnostics of tuberculosis. Responsible for more than 2 million deaths and 8 million new cases annually, tuberculosis is one of the leading infectious diseases in the world. Because of the slow growth rate of the causative agent Mycobacterium tuberculosis, isolation, identification, and drug susceptibility testing of this organism and other clinically important mycobacteria can take several weeks or longer. High-density oligonucleotide arrays have been developed based on 82 unique 16S-rRNA sequences, and these arrays allow for discrimination of 54 mycobacterial species and 51 sequences that contain unique rpoB gene mutations with a turnaround time of only 4h when performed on culture-positive specimens [53, 54]. Using 16S-/23S-rRNA microarrays, different studies were dedicated to the identification and typing of common bacterial pathogens such as Campylobacter spp. [55], Listeria spp. [56, 57], Neisseria meningitidis [58], Chlamydia spp. [59], and S. aureus [60-62] (Table 22.1). A recent study described the use of uropathogen-specific 16S-rDNA genes in a novel electrochemical 16-sensor array to demonstrate that rapid molecular hybridization approaches can be adapted to, room temperature conditions [63]. Microarrays for the detection of pathogens have also increasingly been used in veterinary medicine. A microarray with 32 oligoprobes targeting the 23S-rRNA gene was developed and successfully applied to detect veterinary pathogens responsible for equine abortion from clinical samples [57]. However, the most widespread application of 16S-/23S-rRNA-based microarrays has been in environmental microbiology. A recent study revealed the specific hybridization and detection of microbial 16S-rRNA directly from a total-RNA soil extract, without further purification or removal of soluble soil constituents [64]. In conclusion, the rRNA-based methods have great potential to be incorporated in commercial diagnostic kits for the routine microbiology laboratory.

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