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Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia

Schicklin, Stéphane
Guigon, Ghislaine
Published in Future Microbiology. 2016, vol. 11, no. 3, p. 427-439
Abstract The increasing burden of multidrug-resistant bacteria affects the management of several infections. In order to prescribe adequate antibiotics, clinicians facing severe infections such as hospital-acquired pneumonia (HAP) need to promptly identify the pathogens and know their antibiotic susceptibility profiles (AST), which with conventional microbiology currently requires 24 and 48 h, respectively. Clinical metagenomics, based on whole genome sequencing of clinical samples, could improve the diagnosis of HAP, however, many obstacles remain to be overcome, namely the turn-around time, the quantification of pathogens, the choice of antibiotic resistance determinants (ARDs), the inference of the AST from metagenomic data and the linkage between ARDs and their host. Here, we propose to tackle those issues in a bottom-up, clinically driven approach.
Keywords Anti-Bacterial Agents/therapeutic useBacteria/drug effects/genetics/isolation & purificationComputational BiologyCross Infection/diagnosis/drug therapy/microbiologyDisease ManagementDrug Resistance, Multiple, BacterialEnterobacteriaceae/drug effects/genetics/isolation & purificationGenome, BacterialHigh-Throughput Nucleotide SequencingHumansMetagenomicsPneumonia, Ventilator-Associated/diagnosis/drug therapy/microbiologyRisk Factors
PMID: 26934540
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Research group Analyse génomique et fonctionnelle du staphylocoque doré (604)
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RUPPE, Etienne et al. Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia. In: Future Microbiology, 2016, vol. 11, n° 3, p. 427-439. doi: 10.2217/fmb.15.144 https://archive-ouverte.unige.ch/unige:99531

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Deposited on : 2017-11-22

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