title: The potential of whole genome NGS for infectious disease diagnosis.
abstract: Non-targeted identification of microbes is now possible directly in biological samples, based on whole-genome-NGS (WG-NGS) techniques that allow deep sequencing of nucleic acids, data mining and sorting out of sequences of pathogens without any a priori hypothesis. WG-NGS was first only used as a research tool due to its cost, complexity and lack of standardization. Recent improvements in sample preparation and bioinformatics pipelines and decrease in cost now allow actionable diagnostics in patients. The potency and limits of WG-NGS and possible future indications are discussed here. WG-NGS will likely soon become a standard procedure in microbiological diagnosis.
authors.affiliation: Institut Pasteur, Inserm Unit 1117,  Biology of Infection Unit, Paris, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Lecuit
authors.affiliation: b Biology of Infection Unit , Institut Pasteur, Inserm U1117, Pathogen Discovery Laboratory , Paris , France.|c Pathoquest , Paris , France.
authors.forename: Marc
authors.initials: M
authors.lastname: Eloit
mesh_terms: D003141:Communicable Diseases / Q000175:diagnosis* / Q000382:microbiology / Q000821:virology; D016680:Genome, Bacterial; D016681:Genome, Fungal; D064349:Genome, Microbial; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans
keywords: NGS; bacteria; diagnostic; fungus; infectious diseases; virus