Next- and Third-Generation Sequencing Outperforms Culture-Based Methods in the Diagnosis of Ascitic Fluid Bacterial Infections of ICU Patients

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

(2021) Jinuk Jeong et al.   Scientific Reports

BugSeq: a highly accurate cloud platform for long-read metagenomic analyses

(2021) Jeremy Fan et al.   BMC BIOINFORMATICS

An Epidemiological Meta-Analysis on the Worldwide Prevalence, Resistance, and Outcomes of Spontaneous Bacterial Peritonitis in Cirrhosis

(2021) Phoebe Wen Lin Tay et al.   Frontiers in Medicine

Potential utility of targeted Nanopore sequencing for improving etiologic diagnosis of bacterial and fungal respiratory infection

(2020) Wai Sing Chan et al.   Diagnostic Pathology

Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation

(2020) Aida Iljazovic et al.   Mucosal Immunology

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

(2020) Arne M. Taxt et al.   Scientific Reports

Antimicrobial Susceptibility Patterns and Wild-Type MIC Distributions of Anaerobic Bacteria at a German University Hospital: A Five-Year Retrospective Study (2015–2019)

(2020) Mohamed Tarek Badr et al.   Antibiotics-Basel

Laboratory contamination over time during low‐biomass sample analysis

(2019) Laura S. Weyrich et al.   Molecular Ecology Resources

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

(2019) Themoula Charalampous et al.   NATURE BIOTECHNOLOGY

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Gut microbial composition in patients with psoriasis

(2018) Francisco M. Codoñer et al.   Scientific Reports

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Alteration of the serum microbiome composition in cirrhotic patients with ascites

(2016) Alba Santiago et al.   Scientific Reports

Review article: spontaneous bacterial peritonitis - bacteriology, diagnosis, treatment, risk factors and prevention

(2015) J. B. Dever et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Application of next-generation sequencing to study ascitic microbiome in cirrhotic patients with or without spontaneous bacterial peritonitis

(2015) Ye Feng et al.   JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

Management of cirrhotic ascites

(2015) Julie Steen Pedersen et al.   Therapeutic Advances in Chronic Disease

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

(2014) Martin Laurence et al.   PLoS One

Phylogeny, culturing, and metagenomics of the human gut microbiota

(2014) Alan W. Walker et al.   TRENDS IN MICROBIOLOGY

Paracentesis Is Associated With Reduced Mortality in Patients Hospitalized With Cirrhosis and Ascites

(2013) Eric S. Orman et al.   Clinical Gastroenterology and Hepatology

Diagnosis of Clostridium difficile Infection: an Ongoing Conundrum for Clinicians and for Clinical Laboratories

(2013) C.-A. D. Burnham et al.   CLINICAL MICROBIOLOGY REVIEWS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

2013 WSES guidelines for management of intra-abdominal infections

(2013) Massimo Sartelli et al.   World Journal of Emergency Surgery

Spontaneous bacterial peritonitis

(2012) Mónica Barreales et al.   REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS

Impact of time to antibiotics on survival in patients with severe sepsis or septic shock in whom early goal-directed therapy was initiated in the emergency department*

(2010) David F. Gaieski et al.   CRITICAL CARE MEDICINE

Characterisation of bacteria in ascites—reporting the potential of culture-independent, molecular analysis

(2010) G. B. Rogers et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Infections in Patients With Cirrhosis Increase Mortality Four-Fold and Should Be Used in Determining Prognosis

(2010) Vasiliki Arvaniti et al.   GASTROENTEROLOGY

EASL clinical practice guidelines on the management of ascites, spontaneous bacterial peritonitis, and hepatorenal syndrome in cirrhosis

(2010)   JOURNAL OF HEPATOLOGY

Management of adult patients with ascites due to cirrhosis: An update

(2009) Bruce A. Runyon   HEPATOLOGY

International Study of the Prevalence and Outcomes of Infection in Intensive Care Units

(2009) Jean-Louis Vincent   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION