title: [High-throughput sequencing: towards a genome-based diagnosis in infectious diseases].
abstract: During a pathogen outbreak, the emergency resides in the identification and characterization of the infectious agent. In addition to the traditional phenotypic methods which are still widely used, the molecular biology is nowadays a common approach of clinical microbiology labs and the pathogen can be identified by comparing its molecular fingerprint to a data-bank. High-throughput sequencing should allow overcoming this single identification to exploit the whole information encoded in the pathogen genome. This evolution, supported by an increasing number of proof-of-concept studies, should result in moving from detection through fingerprints to the use of the pathogen whole genome; this forensic profile should allow the adaptation of the treatment to the pathogen specificities. From concept to routine use, many parameters need to be considered to promote high-throughput sequencing as a powerful tool to help physicians and clinicians in microbiological investigations.
authors.affiliation: Gènes Diffusion, Douai, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Audebert
authors.affiliation: U1019, UMR8204, Université de Lille, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France.
authors.forename: David
authors.initials: D
authors.lastname: Hot
authors.affiliation: FRE3642, Université de Lille, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Lemoine
authors.affiliation: FRE3642, Université de Lille, France - Pegase-Biosciences, Institut Pasteur de Lille, 1, rue du professeur Calmette, 59019 Lille, France.
authors.forename: Ségolène
authors.initials: S
authors.lastname: Caboche
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007239:Infections / Q000382:microbiology*; D016415:Sequence Alignment
chemical_list: D004269:DNA, Bacterial