Le séquençage à haut débit dans le diagnostic microbiologique

Abstract

AbstractThe applications of next-generation sequencing (NGS) in health have recently become more widespread, at first in research studies and then in clinical microbiology. The use of NGS has mainly been developed in bacteriology and mycology, especially based on phylogenetic markers (hypervariable regions of rDNA 16S, 18S, or 28S) which allow by metataxonomy, to describe the physiopathological variations of microbiota. By non-targeted metagenomics approaches, the comparison of whole genome NGS data to international databases allows the detection of genomic antimicrobial resistance which is often correlated with the resistance phenotype. Similarly, different strategies to study virulence factors have been developed to compare the genomes of clinical isolates to reference strains and thus to analyze genomic islands. NGS has also shown its efficiency in determining an inter-individual transmission cluster, to identify the source patient or to improve collective management, to search for the etiological agent of an infection.Even though structures such as the Cofrac have taken NGS into account, the lack of standardization limits the routine development of these approaches, due to the need for bioinformatics.