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

Performance and impact of a rapid method combining mass spectrometry and direct antimicrobial susceptibility testing on treatment adequacy of patients with ventilator-associated pneumonia

(2015) M. Le Dorze et al.   CLINICAL MICROBIOLOGY AND INFECTION

Elaboration of a consensual definition of de-escalation allowing a ranking of β-lactams

(2015) E. Weiss et al.   CLINICAL MICROBIOLOGY AND INFECTION

Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: insights using wider sampling frames and next-generation sequencing

(2015) N. Stoesser et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

WGS accurately predicts antimicrobial resistance inEscherichia coli

(2015) Gregory H. Tyson et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting

(2014) N. Stoesser et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Resistome of Pseudomonas aeruginosa in Relationship to Phenotypic Susceptibility

(2014) Veronica N. Kos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing

(2014) N. C. Gordon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid Resistome Fingerprinting and Clonal Lineage Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates by Targeted Next-Generation Sequencing

(2014) F. Arena et al.   JOURNAL OF CLINICAL MICROBIOLOGY

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups

(2014) Tarini Shankar Ghosh et al.   PLoS One

Gram-Stain Plus MALDI-TOF MS (Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry) for a Rapid Diagnosis of Urinary Tract Infection

(2014) Almudena Burillo et al.   PLoS One

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Emergence of Imipenem-Resistant Gram-Negative Bacilli in Intestinal Flora of Intensive Care Patients

(2013) Laurence Armand-Lefèvre et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A comparison of microbiology and demographics among patients with healthcare-associated, hospital-acquired, and ventilator-associated pneumonia: a retrospective analysis of 1184 patients from a large, international study

(2013) Andrew A Quartin et al.   BMC INFECTIOUS DISEASES

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data

(2013) N. Stoesser et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

(2013) H. Hasman et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Clinical Insights from Metagenomic Analysis of Sputum Samples from Patients with Cystic Fibrosis

(2013) Y. W. Lim et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole-Genome Sequencing for Rapid Susceptibility Testing of M. tuberculosis

(2013) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes

(2013) Aimée M. Moore et al.   PLoS One

A pilot study of rapid whole-genome sequencing for the investigation of aLegionellaoutbreak

(2013) Sandra Reuter et al.   BMJ Open

Causes, consequences, and perspectives in the variations of intestinal density of colonization of multidrug-resistant enterobacteria

(2013) Etienne Ruppé et al.   Frontiers in Microbiology

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

(2013) Sandra Reuter et al.   JAMA Internal Medicine

A de novo metagenomic assembly program for shotgun DNA reads

(2012) Binbin Lai et al.   BIOINFORMATICS

Inadequate treatment of ventilator-associated and hospital-acquired pneumonia: Risk factors and impact on outcomes

(2012) Nihal Piskin et al.   BMC INFECTIOUS DISEASES

Analytical validation of a novel high multiplexing real-time PCR array for the identification of key pathogens causative of bacterial ventilator-associated pneumonia and their associated resistance genes

(2012) P. Bogaerts et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Rapid Whole-Genome Sequencing for Investigation of a Suspected Tuberculosis Outbreak

(2012) M. E. Torok et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

High Prevalence of Multidrug-Resistant Nonfermenters in Hospital-acquired Pneumonia in Asia

(2011) Doo Ryeon Chung et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Metagenomic Analysis of Brain Abscesses Identifies Specific Bacterial Associations

(2011) M. Al Masalma et al.   CLINICAL INFECTIOUS DISEASES

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Functional Assay for Rapid Detection of Resistance against  -Lactam Antibiotics

(2011) K. Sparbier et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Validation of the American Thoracic Society–Infectious Diseases Society of America Guidelines for Hospital‐Acquired Pneumonia in the Intensive Care Unit

(2010) Miquel Ferrer et al.   CLINICAL INFECTIOUS DISEASES

Microbial Etiologies of Hospital‐Acquired Bacterial Pneumonia and Ventilator‐Associated Bacterial Pneumonia

(2010) Ronald N. Jones   CLINICAL INFECTIOUS DISEASES

The antibiotic resistome

(2010) Gerard D Wright   Expert Opinion on Drug Discovery

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE