Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078

Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O’Toole 1935) Prévot 1938

(2016) Paul A. Lawson et al.   ANAEROBE

Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5

(2015) Erika van Eijk et al.   BMC GENOMICS

Diversity and Evolution in the Genome of Clostridium difficile

(2015) Daniel R. Knight et al.   CLINICAL MICROBIOLOGY REVIEWS

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Clostridium difficile Infection

(2015) Daniel A. Leffler et al.   NEW ENGLAND JOURNAL OF MEDICINE

Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number

(2015) Zsuzsanna Gyorfy et al.   NUCLEIC ACIDS RESEARCH

Extrachromosomal and integrated genetic elements in Clostridium difficile

(2015) Jacob Amy et al.   PLASMID

Mobile genetic elements in Clostridium difficile and their role in genome function

(2015) Peter Mullany et al.   RESEARCH IN MICROBIOLOGY

Phage tail-like particles kill Clostridium difficile and represent an alternative to conventional antibiotics

(2015) William Sangster et al.   SURGERY

A Modified R-Type Bacteriocin Specifically Targeting Clostridium difficile Prevents Colonization of Mice without Affecting Gut Microbiota Diversity

(2015) Dana Gebhart et al.   mBio

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

(2014) Steven D Brown et al.   Biotechnology for Biofuels

Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011

(2014) C Knetsch et al.   Eurosurveillance

Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor

(2014) S. Hahnke et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

CRISPR–Cas systems: beyond adaptive immunity

(2014) Edze R. Westra et al.   NATURE REVIEWS MICROBIOLOGY

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts

(2014) Pedro H. Oliveira et al.   NUCLEIC ACIDS RESEARCH

Sequence Similarity of Clostridium difficile Strains by Analysis of Conserved Genes and Genome Content Is Reflected by Their Ribotype Affiliation

(2014) Hedwig Kurka et al.   PLoS One

Abundant and Diverse Clustered Regularly Interspaced Short Palindromic Repeat Spacers in Clostridium difficile Strains and Prophages Target Multiple Phage Types within This Pathogen

(2014) K. R. Hargreaves et al.   mBio

CRISPR-Cas systems: new players in gene regulation and bacterial physiology

(2014) Timothy R. Sampson et al.   Frontiers in Cellular and Infection Microbiology

Nucleotide sequence of conjugative prophage Φ1207.3 (formerly Tn1207.3) carrying the mef(A)/msr(D) genes for efflux resistance to macrolides in Streptococcus pyogenes

(2014) Francesco Iannelli et al.   Frontiers in Microbiology

Genetically Diverse Clostridium difficile Strains Harboring Abundant Prophages in an Estuarine Environment

(2013) K. R. Hargreaves et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Asymptomatic Clostridium difficile Colonisation and Onward Transmission

(2013) David W. Eyre et al.   PLoS One

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

Hype or hypervirulence

(2013) Wiep Klaas Smits   Virulence

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

Analysis of a Clostridium difficile PCR ribotype 078 100 kilobase island reveals the presence of a novel transposon, Tn6164

(2012) Jeroen Corver et al.   BMC MICROBIOLOGY

Clostridium difficile genotypes other than ribotype 078 that are prevalent among human, animal and environmental isolates

(2012) Sandra Janezic et al.   BMC MICROBIOLOGY

Editorial Commentary: 027, 078, and Others: Going Beyond the Numbers (and Away From the Hypervirulence)

(2012) F. Barbut et al.   CLINICAL INFECTIOUS DISEASES

The continually evolving Clostridium difficile species

(2012) Michelle D Cairns et al.   Future Microbiology

Novel High-Molecular-Weight, R-Type Bacteriocins of Clostridium difficile

(2012) D. Gebhart et al.   JOURNAL OF BACTERIOLOGY

Macro and Micro Diversity of Clostridium difficile Isolates from Diverse Sources and Geographical Locations

(2012) Richard A. Stabler et al.   PLoS One

Diverse Temperate Bacteriophage Carriage in Clostridium difficile 027 Strains

(2012) Janet Y. Nale et al.   PLoS One

Clostridium difficile in seafood and fish

(2011) Devon Metcalf et al.   ANAEROBE

Metavir: a web server dedicated to virome analysis

(2011) Simon Roux et al.   BIOINFORMATICS

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

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Isolation and characterization of Clostridium difficile from shellfish and marine environments

(2011) Vincenzo Pasquale et al.   FOLIA MICROBIOLOGICA

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Genetic Organisation, Mobility and Predicted Functions of Genes on Integrated, Mobile Genetic Elements in Sequenced Strains of Clostridium difficile

(2011) Michael S. M. Brouwer et al.   PLoS One

The occurrence and high diversity of Clostridium difficile genotypes in rivers

(2010) Valerija Zidaric et al.   ANAEROBE

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

(2010) Heng Li et al.   BIOINFORMATICS

Clostridium difficile in vegetables, Canada

(2010) D.S. Metcalf et al.   LETTERS IN APPLIED MICROBIOLOGY

Self versus non-self discrimination during CRISPR RNA-directed immunity

(2010) Luciano A. Marraffini et al.   NATURE

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Evolutionary dynamics of Clostridium difficile over short and long time scales

(2010) M. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and Enumeration of Clostridium difficile Spores in Retail Beef and Pork

(2009) J. S. Weese et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Multilocus Sequence Typing ofClostridium difficile

(2009) David Griffiths et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Enteric bacterial pathogen detection in southern sea otters (Enhydra lutris nereis) is associated with coastal urbanization and freshwater runoff

(2009) Melissa A. Miller et al.   VETERINARY RESEARCH

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium

(2009) Richard A Stabler et al.   GENOME BIOLOGY

DNAPlotter: circular and linear interactive genome visualization

(2008) T. Carver et al.   BIOINFORMATICS

The bacterial LexA transcriptional repressor

(2008) M. Butala et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Emergence ofClostridium difficileInfection Due to a New Hypervirulent Strain, Polymerase Chain Reaction Ribotype 078

(2008) Abraham Goorhuis et al.   CLINICAL INFECTIOUS DISEASES

CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats

(2008) I. Grissa et al.   NUCLEIC ACIDS RESEARCH