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Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics

Clinical metagenomics (CMg), referred to as the application of next-generation sequencing (NGS) to clinical samples, is a promising tool for the diagnosis of hospital-acquired pneumonia (HAP). Indeed, CMg allows identifying pathogens and antibiotic resistance genes (ARGs), thereby providing the info...

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Autores principales: Ruppé, Etienne, Cherkaoui, Abdessalam, Lazarevic, Vladimir, Emonet, Stéphane, Schrenzel, Jacques
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745473/
https://www.ncbi.nlm.nih.gov/pubmed/29186015
http://dx.doi.org/10.3390/antibiotics6040030
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author Ruppé, Etienne
Cherkaoui, Abdessalam
Lazarevic, Vladimir
Emonet, Stéphane
Schrenzel, Jacques
author_facet Ruppé, Etienne
Cherkaoui, Abdessalam
Lazarevic, Vladimir
Emonet, Stéphane
Schrenzel, Jacques
author_sort Ruppé, Etienne
collection PubMed
description Clinical metagenomics (CMg), referred to as the application of next-generation sequencing (NGS) to clinical samples, is a promising tool for the diagnosis of hospital-acquired pneumonia (HAP). Indeed, CMg allows identifying pathogens and antibiotic resistance genes (ARGs), thereby providing the information required for the optimization of the antibiotic regimen. Hence, provided that CMg would be faster than conventional culture, the probabilistic regimen used in HAP could be tailored faster, which should lead to an expected decrease of mortality and morbidity. While the inference of the antibiotic susceptibility testing from metagenomic or even genomic data is challenging, a limited number of antibiotics are used in the probabilistic regimen of HAP (namely beta-lactams, aminoglycosides, fluoroquinolones, glycopeptides and oxazolidinones). Accordingly, based on the perspective of applying CMg to the early diagnostic of HAP, we aimed at reviewing the performances of whole genomic sequencing (WGS) of the main HAP-causing bacteria (Enterobacteriaceae, Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia and Staphylococcus aureus) for the prediction of susceptibility to the antibiotic families advocated in the probabilistic regimen of HAP.
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spelling pubmed-57454732018-01-02 Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics Ruppé, Etienne Cherkaoui, Abdessalam Lazarevic, Vladimir Emonet, Stéphane Schrenzel, Jacques Antibiotics (Basel) Review Clinical metagenomics (CMg), referred to as the application of next-generation sequencing (NGS) to clinical samples, is a promising tool for the diagnosis of hospital-acquired pneumonia (HAP). Indeed, CMg allows identifying pathogens and antibiotic resistance genes (ARGs), thereby providing the information required for the optimization of the antibiotic regimen. Hence, provided that CMg would be faster than conventional culture, the probabilistic regimen used in HAP could be tailored faster, which should lead to an expected decrease of mortality and morbidity. While the inference of the antibiotic susceptibility testing from metagenomic or even genomic data is challenging, a limited number of antibiotics are used in the probabilistic regimen of HAP (namely beta-lactams, aminoglycosides, fluoroquinolones, glycopeptides and oxazolidinones). Accordingly, based on the perspective of applying CMg to the early diagnostic of HAP, we aimed at reviewing the performances of whole genomic sequencing (WGS) of the main HAP-causing bacteria (Enterobacteriaceae, Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia and Staphylococcus aureus) for the prediction of susceptibility to the antibiotic families advocated in the probabilistic regimen of HAP. MDPI 2017-11-29 /pmc/articles/PMC5745473/ /pubmed/29186015 http://dx.doi.org/10.3390/antibiotics6040030 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Ruppé, Etienne
Cherkaoui, Abdessalam
Lazarevic, Vladimir
Emonet, Stéphane
Schrenzel, Jacques
Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics
title Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics
title_full Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics
title_fullStr Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics
title_full_unstemmed Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics
title_short Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics
title_sort establishing genotype-to-phenotype relationships in bacteria causing hospital-acquired pneumonia: a prelude to the application of clinical metagenomics
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745473/
https://www.ncbi.nlm.nih.gov/pubmed/29186015
http://dx.doi.org/10.3390/antibiotics6040030
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