High-throughput sequencing and clinical microbiology

High throughput sequencing High-throughput sequencing is an umbrella term applied to new sequencing technologies that deliver sequence data hundreds or thousands times more cheaply and speedily than traditional approaches. Three competing technologies have achieved widespread uptake: the Roche 454 platform, the Solexa/Illumina platform and Life Technologies SOLiD platform.

Genome sequencing has already transformed the study of microbial pathogens. For the first time, sequencing on a genomic scale now falls within the technical capability of the average university department and within the financial envelope of a modest research grant. Now that bacterial genomes can be sequenced in days or weeks rather than months or years, microbial genomics is at last poised to make a direct impact in clinical diagnostics, epidemiology and infection control. High-throughput sequencing also stands to revolutionise our view of the host response to infection and vaccination.

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr Opin Microbiol. Sep 13 2010
High-throughput sequencing is sweeping through clinical microbiology, transforming our discipline in its wake. It is already providing an enhanced view of pathogen biology through rapid and inexpensive whole-genome sequencing and more sophisticated applications such as RNA-seq. It also promises to deliver high-resolution genomic epidemiology as the ultimate typing method for bacteria. However, the most revolutionary effect of this ‘disruptive technology’ is likely to be creation of a novel sequence-based, culture-independent diagnostic microbiology that incorporates microbial community profiling, metagenomics and single-cell genomics. We should prepare for the coming ‘technological singularity’ in sequencing, when this technology becomes so fast and so cheap that it threatens to out-compete existing diagnostic and typing methods in microbiology.

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