Bone and joint infections in hospitalized patients in France, 2008: clinical and economic outcomes, Journal of Hospital Infection, vol.82, issue.1, pp.40-48, 2012. ,
DOI : 10.1016/j.jhin.2012.04.025
Clinical metagenomics for the management of hospital-and healthcareacquired pneumonia, Future Microbiol. Ahead of print, 2015. ,
Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples, Journal of Clinical Microbiology, vol.52, issue.1, pp.139-146, 2014. ,
DOI : 10.1128/JCM.02452-13
Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing, Journal of Antimicrobial Chemotherapy, vol.72, issue.1, pp.10-1093, 2016. ,
DOI : 10.1093/jac/dkw397
Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing, New England Journal of Medicine, vol.370, issue.25, pp.2408-2417, 2014. ,
DOI : 10.1056/NEJMoa1401268
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4134948
Next-Generation Sequencing for Diagnosis and Tailored Therapy: A Case Report of Astrovirus-Associated Progressive Encephalitis, Journal of the Pediatric Infectious Diseases Society, vol.4, issue.3, pp.53-57, 2015. ,
DOI : 10.1093/jpids/piv040
Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia, Scientific Reports, vol.21, issue.4679, p.23532, 2016. ,
DOI : 10.1089/cmb.2014.0029
Live rubella virus vaccine long-term persistence as an antigenic trigger of cutaneous granulomas in patients with primary immunodeficiency, Clinical Microbiology and Infection, vol.20, issue.10, pp.656-663, 2014. ,
DOI : 10.1111/1469-0691.12573
Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak, New England Journal of Medicine, vol.366, issue.24, pp.2267-2275, 2012. ,
DOI : 10.1056/NEJMoa1109910
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing, Journal of Antimicrobial Chemotherapy, vol.68, issue.4, pp.771-777, 2013. ,
DOI : 10.1093/jac/dks496
Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing, Journal of Clinical Microbiology, vol.52, issue.4, pp.1182-1191, 2014. ,
DOI : 10.1128/JCM.03117-13
URL : http://jcm.asm.org/content/52/4/1182.full.pdf
Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data, Journal of Antimicrobial Chemotherapy, vol.68, issue.10, pp.2234-2244, 2013. ,
DOI : 10.1093/jac/dkt180
URL : https://academic.oup.com/jac/article-pdf/68/10/2234/16862715/dkt180.pdf
WGS accurately predicts antimicrobial resistance in Escherichia coli, J. Antimicrob. Chemother, pp.10-1093, 2015. ,
DOI : 10.1093/jac/dkv186
URL : https://academic.oup.com/jac/article-pdf/70/10/2763/2476476/dkv186.pdf
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis, Nature Communications, vol.52, p.10063, 2015. ,
DOI : 10.1128/JCM.00262-14
URL : http://www.nature.com/articles/ncomms10063.pdf
The Resistome of Pseudomonas aeruginosa in Relationship to Phenotypic Susceptibility, Antimicrobial Agents and Chemotherapy, vol.59, issue.1, pp.427-436, 2015. ,
DOI : 10.1128/AAC.03954-14
Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients, Frontiers in Cellular and Infection Microbiology, vol.9, p.65, 2014. ,
DOI : 10.1186/1471-2180-9-259
Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples, PLoS ONE, vol.8, issue.4, p.34605, 2012. ,
DOI : 10.1371/journal.pone.0034605.s006
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses, BMC Biology, vol.5, issue.1, 2014. ,
DOI : 10.1371/journal.pcbi.1000352
URL : http://doi.org/10.1186/s12915-014-0087-z
ABSTRACT, mSystems, vol.1, issue.3, pp.50-66, 2016. ,
DOI : 10.1128/mSystems.00050-16
Comparison of DNA Extraction Methods in Analysis of Salivary Bacterial Communities, PLoS ONE, vol.7, issue.7, p.67699, 2013. ,
DOI : 10.1371/journal.pone.0067699.s005
Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, issue.15, pp.2114-2120, 2014. ,
DOI : 10.1093/bioinformatics/btu170
URL : https://academic.oup.com/bioinformatics/article-pdf/30/15/2114/17143152/btu170.pdf
Metagenomic microbial community profiling using unique clade-specific marker genes, Nature Methods, vol.2008, issue.8, pp.811-814, 2012. ,
DOI : 10.1093/nar/gkn879
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443552
MetaPhlAn2 for enhanced metagenomic taxonomic profiling, Nature Methods, vol.486, issue.10, pp.902-903, 2015. ,
DOI : 10.1126/science.1171700
Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome Biology, vol.15, issue.3, p.46, 2014. ,
DOI : 10.1186/1471-2105-12-385
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2014-15-3-r46?site=genomebiology.biomedcentral.com
metaSPAdes: a new versatile metagenomic assembler, Genome Research, vol.5, issue.5, 2016. ,
DOI : 10.1101/gr.074492.107
URL : http://doi.org/10.1101/gr.213959.116
Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, issue.14, pp.2068-2069, 2014. ,
DOI : 10.1093/bioinformatics/btu153
URL : https://academic.oup.com/bioinformatics/article-pdf/30/14/2068/7250406/btu153.pdf
QUAST: quality assessment tool for genome assemblies, Bioinformatics, vol.29, issue.8, pp.1072-1075, 2013. ,
DOI : 10.1093/bioinformatics/btt086
URL : https://academic.oup.com/bioinformatics/article-pdf/29/8/1072/17106244/btt086.pdf
Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012. ,
DOI : 10.1093/bioinformatics/btp352
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381
Identification of acquired antimicrobial resistance genes, Journal of Antimicrobial Chemotherapy, vol.67, issue.11, pp.2640-2644, 2012. ,
DOI : 10.1093/jac/dks261
Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora, Science, vol.31, issue.13, pp.1128-1131, 2009. ,
DOI : 10.1093/nar/gkg500
Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes, PLoS ONE, vol.57, issue.11, p.78822, 2013. ,
DOI : 10.1371/journal.pone.0078822.s002
URL : http://doi.org/10.1371/journal.pone.0078822
Interconnected microbiomes and resistomes in low-income human habitats, Nature, vol.7, issue.7602, pp.212-216, 2016. ,
DOI : 10.1371/journal.pone.0038581
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869995
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, vol.22, issue.13, pp.1658-1659, 2006. ,
DOI : 10.1093/bioinformatics/btl158
Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, vol.11, issue.1, 2010. ,
DOI : 10.1186/1471-2105-11-119
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-119?site=bmcbioinformatics.biomedcentral.com
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, vol.27, issue.21, pp.2987-2993, 2011. ,
DOI : 10.1093/bioinformatics/btr509
URL : https://academic.oup.com/bioinformatics/article-pdf/27/21/2987/577342/btr509.pdf
Haplotype-based variant detection from short-read sequencing, 2012. ,
Using Tablet for visual exploration of second-generation sequencing data, Briefings in Bioinformatics, vol.14, issue.2, pp.193-202, 2013. ,
DOI : 10.1093/bib/bbs012