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Pathogens 2014, 3(2), 258-279; doi:10.3390/pathogens3020258

High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology

1
FRE 3642 Molecular and Cellular Medecine, CNRS, Institut Pasteur de Lille and University Lille Nord de France, Lille 59019, France
2
GENES DIFFUSION, 3595, route de Tournai, DOUAI 59501, France
3
Transcriptomics and Applied Genomics, Center of Infection and Immunity of Lille, INSERM U1019, CNRS UMR8204, Institut Pasteur de Lille, Univ. Lille Nord de France, Lille 59019, France
4
PEGASE-Biosciences, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, Lille 59019, France
*
Author to whom correspondence should be addressed.
Received: 20 November 2013 / Revised: 28 February 2014 / Accepted: 20 March 2014 / Published: 2 April 2014
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Abstract

The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic agents. Many studies have demonstrated that data obtained from HTS analysis have allowed genome-based diagnosis, which has been consistent with phenotypic observations. These proofs of concept are probably the first steps toward the future of clinical microbiology. From concept to routine use, many parameters need to be considered to promote HTS as a powerful tool to help physicians and clinicians in microbiological investigations. This review highlights the milestones to be completed toward this purpose. View Full-Text
Keywords: high-throughput sequencing; whole genome sequencing; pathogenomics; bioinformatics; analysis pipeline; P4-medicine; genome-based diagnosis high-throughput sequencing; whole genome sequencing; pathogenomics; bioinformatics; analysis pipeline; P4-medicine; genome-based diagnosis
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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Caboche, S.; Audebert, C.; Hot, D. High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology. Pathogens 2014, 3, 258-279.

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