Abstract
1 Biology of Infection Unit, Institut Pasteur, Paris, France 2 Inserm U1117, Paris, France 3 Sorbonne Paris Cite, Institut Imagine, Paris Descartes University, Paris, France 4 Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Paris, France 5 Laboratory of Pathogen Discovery, Department of Virology, Institut Pasteur, Paris, France 6 PathoQuest, Paris, France *Correspondence: marc.eloit@pasteur.fr
Highlights
The diagnosis of infectious diseases by whole genome generation sequencing: a new era is opening
The demonstration of the microbial origin of diseases and their diagnosis were initially based on the demonstration of the presence of a given pathogen in a given clinical sample, and was first dominated by culture assay for bacteria and later for viruses
The range of multiplex PCR can be considerably improved by designing primers targeting numerous pathogens and varied loci within pathogens and resolving these amplicons using electrospray ionization-mass spectrometry (Wolk et al, 2012) or next generation sequencing (NGS) (Arena et al, 2014)
Summary
The diagnosis of infectious diseases by whole genome generation sequencing: a new era is opening. As in other medical fields, the availability of generation sequencing (NGS) techniques is about to revolutionize diagnostics of infectious diseases. Use of NGS has increased the depth of sequencing by several orders of magnitude and thereby the capacity to detect rare species.
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