title: Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia.
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.
authors.affiliation: Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland.
authors.forename: Etienne
authors.initials: E
authors.lastname: Ruppé
authors.affiliation: Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland.
authors.forename: Damien
authors.initials: D
authors.lastname: Baud
authors.affiliation: Bioinformatics Research Department, bioMérieux, 69280 Marcy l'Etoile, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Schicklin
authors.affiliation: Bioinformatics Research Department, bioMérieux, 69280 Marcy l'Etoile, France.
authors.forename: Ghislaine
authors.initials: G
authors.lastname: Guigon
authors.affiliation: Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, rue Gabrielle-Perret-Gentil 4, 1205 Geneva, Switzerland.|Bacteriology Lab, Service of Laboratory Medicine, Department of Genetics & Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland.
authors.forename: Jacques
authors.initials: J
authors.lastname: Schrenzel
mesh_terms: D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D001419:Bacteria / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D019295:Computational Biology; D003428:Cross Infection / Q000175:diagnosis* / Q000188:drug therapy / Q000382:microbiology; D019468:Disease Management; D024901:Drug Resistance, Multiple, Bacterial; D004755:Enterobacteriaceae / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D056186:Metagenomics; D053717:Pneumonia, Ventilator-Associated / Q000175:diagnosis* / Q000188:drug therapy / Q000382:microbiology; D012307:Risk Factors
chemical_list: D000900:Anti-Bacterial Agents
keywords: HAP; HCAP; VAP; antibiotic resistance; diagnosis; next-generation sequencing