Carriage of Extended-Spectrum Beta-Lactamase-Plasmids Does Not Reduce Fitness but Enhances Virulence in Some Strains of Pandemic E. coli Lineages

Escherichia coli ST131, an Intriguing Clonal Group

(2014) M.-H. Nicolas-Chanoine et al.   CLINICAL MICROBIOLOGY REVIEWS

Cyclic-di-GMP signalling and biofilm-related properties of the Shiga toxin-producing 2011 German outbreak Escherichia coli O104:H4

(2014) A. M. Richter et al.   EMBO Molecular Medicine

CTX-M-15-D-ST648 Escherichia coli from companion animals and horses: another pandemic clone combining multiresistance and extraintestinal virulence?

(2014) C. Ewers et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

(2014) Astrid von Mentzer et al.   NATURE GENETICS

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

SPSS survival manual: a step by step guide to data analysis using IBM SPSS

(2013)   AUSTRALIAN AND NEW ZEALAND JOURNAL OF PUBLIC HEALTH

opm: an R package for analysing OmniLog(R) phenotype microarray data

(2013) L. A. I. Vaas et al.   BIOINFORMATICS

Repression of Flagellar Genes in Exponential Phase by CsgD and CpxR, Two Crucial Modulators of Escherichia coli Biofilm Formation

(2013) O. Dudin et al.   JOURNAL OF BACTERIOLOGY

ESBL-plasmids carrying toxin-antitoxin systems can be “cured” of wild-type Escherichia coli using a heat technique

(2013) Katharina Schaufler et al.   Gut Pathogens

Prevalent combination of virulence and plasmidic-encoded resistance in ST 131Escherichia colistrains

(2013) Vera Calhau et al.   Virulence

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Extended-spectrum β-lactamase-producing and AmpC-producing Escherichia coli from livestock and companion animals, and their putative impact on public health: a global perspective

(2012) C. Ewers et al.   CLINICAL MICROBIOLOGY AND INFECTION

Identification of acquired antimicrobial resistance genes

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

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RNA snap ™: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria

(2012) Mark B. Stead et al.   NUCLEIC ACIDS RESEARCH

Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics

(2012) Lea A. I. Vaas et al.   PLoS One

Small RNAs and their role in biofilm formation

(2012) Jacob R. Chambers et al.   TRENDS IN MICROBIOLOGY

Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture

(2012) Claudia Seiler et al.   Frontiers in Microbiology

Extraintestinal Pathogenic Escherichia coli: A Combination of Virulence with Antibiotic Resistance

(2012) Johann D. D. Pitout   Frontiers in Microbiology

Identification and removal of ribosomal RNA sequences from metatranscriptomes

(2011) Robert Schmieder et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

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

Role of the Biofilm Master Regulator CsgD in Cross-Regulation between Biofilm Formation and Flagellar Synthesis

(2011) H. Ogasawara et al.   JOURNAL OF BACTERIOLOGY

The CTX-M Conundrum: Dissemination of Plasmids and Escherichia coli Clones

(2011) Umaer Naseer et al.   Microbial Drug Resistance

Escherichia coliSequence Type ST131 as the Major Cause of Serious Multidrug‐ResistantE. coliInfections in the United States

(2010) James R. Johnson et al.   CLINICAL INFECTIOUS DISEASES

Emergence of human pandemic O25:H4-ST131 CTX-M-15 extended-spectrum-β-lactamase-producing Escherichia coli among companion animals

(2010) Christa Ewers et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Characterization of Extended-Spectrum β-Lactamases Produced by Escherichia coli Isolated from Hospitalized and Nonhospitalized Patients: Emergence of CTX-M-15-Producing Strains Causing Urinary Tract Infections

(2010) Annemieke Smet et al.   Microbial Drug Resistance

Antibiotic resistance and its cost: is it possible to reverse resistance?

(2010) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Complete Nucleotide Sequence of CTX-M-15-Plasmids from Clinical Escherichia coli Isolates: Insertional Events of Transposons and Insertion Sequences

(2010) Annemieke Smet et al.   PLoS One

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Increased Antibiotic Resistance of Escherichia coli in Mature Biofilms

(2009) A. Ito et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Biofilm formation as a novel phenotypic feature of adherent-invasive Escherichia coli (AIEC)

(2009) Margarita Martinez-Medina et al.   BMC MICROBIOLOGY

Extended-Spectrum  -Lactamase Production Is Associated with an Increase in Cell Invasion and Expression of Fimbrial Adhesins in Klebsiella pneumoniae

(2008) H. Sahly et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Isolation and Characterization of Intestinal Escherichia coli Clones from Wild Boars in Germany

(2008) P. Schierack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The R1 Conjugative Plasmid Increases Escherichia coli Biofilm Formation through an Envelope Stress Response

(2008) X. Yang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli

(2008) T. May et al.   JOURNAL OF BACTERIOLOGY