Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods

Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance

(2020) Ashley L. Cooper et al.   Frontiers in Microbiology

The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country

(2020) Stéphanie Nouws et al.   Foods

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates

(2020) Stéphanie Nouws et al.   Scientific Reports

Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: Neisseria meningitidis as a Proof-of-Concept

(2019) Bert Bogaerts et al.   Frontiers in Microbiology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017

(2019) Narjol González-Escalona et al.   PLoS One

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation

(2019) Helena M. B. Seth-Smith et al.   Frontiers in Public Health

From genotype to antibiotic susceptibility phenotype in the order Enterobacterales: a clinical perspective

(2019) E. Ruppé et al.   CLINICAL MICROBIOLOGY AND INFECTION

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

(2019) James J Davis et al.   NUCLEIC ACIDS RESEARCH

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

(2019) Zhemin Zhou et al.   GENOME RESEARCH

Genomics of foodborne pathogens for microbial food safety

(2018) Marc W Allard et al.   CURRENT OPINION IN BIOTECHNOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Twenty-seven years of screening for Shiga toxin-producing Escherichia coli in a university hospital. Brussels, Belgium, 1987-2014

(2018) Klara De Rauw et al.   PLoS One

A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica

(2018) Anne-Catherine Portmann et al.   Frontiers in Microbiology

Rapid and precise alignment of raw reads against redundant databases with KMA

(2018) Philip T. L. C. Clausen et al.   BMC BIOINFORMATICS

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

(2018) Zhemin Zhou et al.   GENOME RESEARCH

Genome-based prediction of bacterial antibiotic resistance

(2018) Michelle Su et al.   JOURNAL OF CLINICAL MICROBIOLOGY

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

(2017) Ea Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Reprint of “Application of next generation sequencing in clinical microbiology and infection prevention”

(2017) Ruud H. Deurenberg et al.   JOURNAL OF BIOTECHNOLOGY

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory

(2017) Varvara K. Kozyreva et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial

(2017) Alexander Mellmann et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Validation of Whole-Genome Sequencing for Identification and Characterization of Shiga Toxin-Producing Escherichia coli To Produce Standardized Data To Enable Data Sharing

(2017) Anne Holmes et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A RESTful application programming interface for the PubMLST molecular typing and genome databases

(2017) Keith A. Jolley et al.   Database-The Journal of Biological Databases and Curation

A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens

(2017) Lee S. Katz et al.   Frontiers in Microbiology

The Validation and Implications of Using Whole Genome Sequencing as a Replacement for Traditional Serotyping for a National Salmonella Reference Laboratory

(2017) Chris A. Yachison et al.   Frontiers in Microbiology

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance

(2017) Ruth E. Timme et al.   PeerJ

Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution

(2017) J A Carriço et al.   Eurosurveillance

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation

(2016) Brendan R. Jackson et al.   CLINICAL INFECTIOUS DISEASES

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

(2016) J. Ronholm et al.   CLINICAL MICROBIOLOGY REVIEWS

Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data

(2016) Philip T. L. C. Clausen et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

(2016) Marjolein F. Q. Kluytmans-van den Bergh et al.   JOURNAL OF CLINICAL MICROBIOLOGY

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Implementation of Whole Genome Sequencing (WGS) for Identification and Characterization of Shiga Toxin-Producing Escherichia coli (STEC) in the United States

(2016) Rebecca L. Lindsey et al.   Frontiers in Microbiology

Whole-Genome Sequencing for National Surveillance of Shiga Toxin–ProducingEscherichia coliO157

(2015) Timothy J. Dallman et al.   CLINICAL INFECTIOUS DISEASES

Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

(2015) Katrine G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data

(2015) Will Rowe et al.   PLoS One

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

(2014) K. G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms

(2014) Rolf S. Kaas et al.   PLoS One

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

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

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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

(2013) Daniel Garijo et al.   PLoS One

Public Health Genomics and the New Molecular Epidemiology of Bacterial Pathogens

(2013) M.W. Gilmour et al.   Public Health Genomics

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

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

Identification of acquired antimicrobial resistance genes

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

Incidence and Virulence Determinants of Verocytotoxin-Producing Escherichia coli Infections in the Brussels-Capital Region, Belgium, in 2008-2010

(2012) G. Buvens et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Thrombotic microangiopathy and associated renal disorders

(2012) T. Barbour et al.   NEPHROLOGY DIALYSIS TRANSPLANTATION

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Shiga Toxin Subtypes Display Dramatic Differences in Potency

(2011) Cynthia A. Fuller et al.   INFECTION AND IMMUNITY

Epidemic Profile of Shiga-Toxin–ProducingEscherichia coliO104:H4 Outbreak in Germany

(2011) Christina Frank et al.   NEW ENGLAND JOURNAL OF MEDICINE

Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome

(2011) K. A. Karberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains

(2008) Françoise Jaureguy et al.   BMC GENOMICS