Origin and Evolution of Hybrid Shiga Toxin-Producing and Uropathogenic Escherichia coli Strains of Sequence Type 141

Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci

(2019) Veronika Tchesnokova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli (IPEC) and Extraintestinal Pathogenic Escherichia coli (ExPEC) virulence factors isolated from human faecal samples

(2018) Bjørn-Arne Lindstedt et al.   BMC INFECTIOUS DISEASES

RefSeq: an update on prokaryotic genome annotation and curation

(2017) Daniel H Haft et al.   NUCLEIC ACIDS RESEARCH

Origin, evolution, and global transmission of community-acquiredStaphylococcus aureusST8

(2017) Lena Strauß et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting

(2016) Alexander Mellmann et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Detecting Staphylococcus aureus Virulence and Resistance Genes: a Comparison of Whole-Genome Sequencing and DNA Microarray Technology

(2016) Lena Strauß et al.   JOURNAL OF CLINICAL MICROBIOLOGY

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai–Tibet plateau of China

(2016) Shan Lu et al.   Emerging Microbes & Infections

Heteropathogenic virulence and phylogeny reveal phased pathogenic metamorphosis inEscherichia coliO2:H6

(2014) Martina Bielaszewska et al.   EMBO Molecular Medicine

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

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

Enterohemorrhagic Escherichia coli O26:H11/H−: A New Virulent Clone Emerges in Europe

(2013) Martina Bielaszewska et al.   CLINICAL INFECTIOUS DISEASES

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Point Mutations in FimH Adhesin of Crohn's Disease-Associated Adherent-Invasive Escherichia coli Enhance Intestinal Inflammatory Response

(2013) Nicolas Dreux et al.   PLoS Pathogens

The enemy within us: lessons from the 2011 EuropeanEscherichia coliO104:H4 outbreak

(2012) Helge Karch et al.   EMBO Molecular Medicine

Multicenter Evaluation of a Sequence-Based Protocol for Subtyping Shiga Toxins and Standardizing Stx Nomenclature

(2012) F. Scheutz et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC)

(2011) Elzbieta Brzuszkiewicz et al.   ARCHIVES OF MICROBIOLOGY

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

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

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

Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study

(2011) Martina Bielaszewska et al.   LANCET INFECTIOUS DISEASES

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

(2011) Alexander Mellmann et al.   PLoS One

Comparative analysis of virulence genes, genetic diversity, and phylogeny of Shiga toxin 2g and heat-stable enterotoxin STIa encoding Escherichia coli isolates from humans, animals, and environmental sources

(2010) Rita Prager et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Characterization of Shiga Toxin–Producing Escherichia coli Strains Isolated from Swine Feces

(2008) Pina M. Fratamico et al.   Foodborne Pathogens and Disease

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH