Preprint Review Version 1 This version is not peer-reviewed

From Genotype to Phenotype: A Clinical Perspective for Hospital-Acquired Pneumonia

Version 1 : Received: 29 September 2017 / Approved: 30 September 2017 / Online: 30 September 2017 (04:49:23 CEST)

A peer-reviewed article of this Preprint also exists.

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. 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.

Journal reference: Antibiotics 2017, 6, 30
DOI: 10.3390/antibiotics6040030

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 in 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.

Subject Areas

next-generation sequencing; whole-genome sequencing; hospital-acquired pneumonia; antibiotic resistance; prediction; clinical metagenomics

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