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Antibiotics 2017, 6(4), 30; doi:10.3390/antibiotics6040030

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

1
Genomic Research Laboratory, Geneva University Hospitals, CMU-9F, Rue Michel Servet 1, CH-1211 Geneva 14, Switzerland
2
Laboratory of Bacteriology, University Hospitals, Rue Gabrielle Perret-Gentil 4, CH-1211 Geneva 14, Switzerland
3
Service of Infectious Diseases, Geneva University Hospitals, Rue Gabrielle Perret-Gentil 4, CH-1211 Geneva 14, Switzerland
*
Author to whom correspondence should be addressed.
Received: 29 September 2017 / Revised: 17 November 2017 / Accepted: 20 November 2017 / Published: 29 November 2017
(This article belongs to the Special Issue Top 35 of Antibiotics Travel Awards 2017)
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Abstract

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. View Full-Text
Keywords: next-generation sequencing; whole-genome sequencing; hospital-acquired pneumonia; antibiotic resistance; prediction next-generation sequencing; whole-genome sequencing; hospital-acquired pneumonia; antibiotic resistance; prediction
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Ruppé, E.; Cherkaoui, A.; Lazarevic, V.; Emonet, S.; Schrenzel, J. Establishing Genotype-to-Phenotype Relationships in Bacteria Causing Hospital-Acquired Pneumonia: A Prelude to the Application of Clinical Metagenomics. Antibiotics 2017, 6, 30.

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