Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.

Détails

Ressource 1Télécharger: 28639162.pdf (814.46 [Ko])
Etat: Public
Version: Final published version
ID Serval
serval:BIB_49356DED3F2E
Type
Article: article d'un périodique ou d'un magazine.
Sous-type
Synthèse (review): revue aussi complète que possible des connaissances sur un sujet, rédigée à partir de l'analyse exhaustive des travaux publiés.
Collection
Publications
Institution
Titre
Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.
Périodique
European journal of clinical microbiology & infectious diseases
Auteur(s)
Tagini F., Greub G.
ISSN
1435-4373 (Electronic)
ISSN-L
0934-9723
Statut éditorial
Publié
Date de publication
11/2017
Peer-reviewed
Oui
Volume
36
Numéro
11
Pages
2007-2020
Langue
anglais
Notes
Publication types: Journal Article ; Review
Publication Status: ppublish
Résumé
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
Mots-clé
Bacteria/genetics, Bacteria/pathogenicity, Base Sequence, Genome, Bacterial/genetics, High-Throughput Nucleotide Sequencing/methods, Humans, Multilocus Sequence Typing/methods, Virulence/genetics, Clinical microbiology, Genomics, Next-generation sequencing, Whole-genome sequencing
Pubmed
Web of science
Open Access
Oui
Création de la notice
06/07/2017 18:43
Dernière modification de la notice
20/08/2019 14:56
Données d'usage