Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges

Genomics of foodborne pathogens for microbial food safety

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

A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study

(2018) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Impact of the choice of reference genome on the ability of the core genome SNV methodology to distinguish strains of Salmonella enterica serovar Heidelberg

(2018) Valentine Usongo et al.   PLoS One

Intraclade Variability in Toxin Production and Cytotoxicity of Bacillus cereus Group Type Strains and Dairy-Associated Isolates

(2018) Rachel A. Miller et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Investigation using whole genome sequencing of a prolonged restaurant outbreak of Salmonella Typhimurium linked to the building drainage system, England, February 2015 to March 2016

(2017) John Mair-Jenkins et al.   Eurosurveillance

Whole genome sequencing (WGS) for food-borne pathogen surveillance and control – taking the pulse

(2017) Jacob Moran-Gilad   Eurosurveillance

Proposal of nine novel species of the Bacillus cereus group

(2017) Yang Liu et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Singleton Sequence Type 382, an Emerging Clonal Group of Listeria monocytogenes Associated with Three Multistate Outbreaks Linked to Contaminated Stone Fruit, Caramel Apples, and Leafy Green Salad

(2017) Yi Chen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evaluation of Two Standard and Two Chromogenic Selective Media for Optimal Growth and Enumeration of Isolates of 16 Unique Bacillus Species

(2017) M. Shahjahan Kabir et al.   JOURNAL OF FOOD PROTECTION

treespace : Statistical exploration of landscapes of phylogenetic trees

(2017) Thibaut Jombart et al.   Molecular Ecology Resources

Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States

(2017) Yi Chen et al.   PLoS One

Precision food safety: A systems approach to food safety facilitated by genomics tools

(2017) Jasna Kovac et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation

(2017) Rosemary M. McCloskey et al.   PLoS Computational Biology

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

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

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access

(2017) Eduardo N. Taboada et al.   Frontiers in Microbiology

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data

(2017) Sarah Sandmann et al.   Scientific Reports

Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade

(2016) Jasna Kovac et al.   BMC GENOMICS

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

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

Bacillus cereus-induced food-borne outbreaks in France, 2007 to 2014: epidemiology and genetic characterisation

(2016) Benjamin Glasset et al.   Eurosurveillance

Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments

(2016) Rachel A. Miller et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks

(2016) Brigida Rusconi et al.   Frontiers in Microbiology

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome: Table 1

(2015) Shea N Gardner et al.   BIOINFORMATICS

Is Cytotoxin K from Bacillus cereus a bona fide enterotoxin?

(2015) Virginie Castiaux et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes

(2015) Jason C. Kwong et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance

(2015) Anne Holmes et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

(2015) Angela J. Taylor et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Tracing Origins of theSalmonellaBareilly Strain Causing a Food-borne Outbreak in the United States

(2015) Maria Hoffmann et al.   JOURNAL OF INFECTIOUS DISEASES

Food–bacteria interplay: pathometabolism of emetic Bacillus cereus

(2015) Monika Ehling-Schulz et al.   Frontiers in Microbiology

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

(2015) Nathan D. Olson et al.   Frontiers in Genetics

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   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

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

(2014) Arthur W. Pightling et al.   PLoS One

EmeticBacillus cereusAre More Volatile Than Thought: Recent Foodborne Outbreaks and Prevalence Studies in Bavaria (2007–2013)

(2014) Ute Messelhäusser et al.   Biomed Research International

Foodborne Disease Outbreaks Caused by Bacillus cereus, Clostridium perfringens, and Staphylococcus aureus--United States, 1998-2008

(2013) S. D. Bennett et al.   CLINICAL INFECTIOUS DISEASES

PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

(2013) Marti J. Anderson et al.   ECOLOGICAL MONOGRAPHS

Diversity ofBacillus cereusgroup strains is reflected in their broad range of pathogenicity and diverse ecological lifestyles

(2013) Siele Ceuppens et al.   FEMS MICROBIOLOGY ECOLOGY

Food Microbe Tracker: A Web-Based Tool for Storage and Comparison of Food-Associated Microbes

(2013) PAJAU VANGAY et al.   JOURNAL OF FOOD PROTECTION

Concerted Action of Sphingomyelinase and Non-Hemolytic Enterotoxin in Pathogenic Bacillus cereus

(2013) Viktoria M. Doll et al.   PLoS One

When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes

(2013) Shea N. Gardner et al.   PLoS One

Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations

(2013) Guillermo Jiménez et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Identification and Characterization of Psychrotolerant Sporeformers Associated with Fluid Milk Production and Processing

(2012) Reid A. Ivy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacillus cytotoxicus sp. nov. is a novel thermotolerant species of the Bacillus cereus Group occasionally associated with food poisoning

(2012) M.-H. Guinebretiere et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Efficient Isolation and Identification of Bacillus cereus Group

(2012) Sandra M. Tallent et al.   JOURNAL OF AOAC INTERNATIONAL

Can Bacillus cereus Food Poisoning Cause Sudden Death?

(2012) H. Sanaei-Zadeh   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

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Sudden Death of a Young Adult Associated with Bacillus cereus Food Poisoning

(2011) M. Naranjo et al.   JOURNAL OF CLINICAL MICROBIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Ability of Bacillus cereus Group Strains To Cause Food Poisoning Varies According to Phylogenetic Affiliation (Groups I to VII) Rather than Species Affiliation

(2010) M.-H. Guinebretiere et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Mesoporous silica nanoparticles enhance MTT formazan exocytosis in HeLa cells and astrocytes

(2009) Matthieu Fisichella et al.   TOXICOLOGY IN VITRO

Ecological diversification in the Bacillus cereus Group

(2007) Marie-Hélène Guinebretière et al.   ENVIRONMENTAL MICROBIOLOGY