title: High-throughput sequencing and clinical microbiology: progress, opportunities and challenges.
abstract: 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.
authors.affiliation: School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom. m.pallen@bham.ac.uk
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Loman
authors.forename: Charles W
authors.initials: CW
authors.lastname: Penn
mesh_terms: D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D008828:Microbiological Techniques / Q000379:methods*; D010641:Phenotype; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA