A comprehensive and high-quality collection of Escherichia coli genomes and their genes

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

(2020) Marie Touchon et al.   PLoS Genetics

Ultrafast search of all deposited bacterial and viral genomic data

(2019) Phelim Bradley et al.   NATURE BIOTECHNOLOGY

Fast and flexible bacterial genomic epidemiology with PopPUNK

(2019) John A. Lees et al.   GENOME RESEARCH

Characterisation and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential

(2019) Olivier Clermont et al.   ENVIRONMENTAL MICROBIOLOGY

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

Integrating long-range connectivity information into de Bruijn graphs

(2018) Isaac Turner et al.   BIOINFORMATICS

Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity

(2018) Fabrizio Menardo et al.   BMC BIOINFORMATICS

Going around in circles: virulence plasmids in enteric pathogens

(2018) Giulia Pilla et al.   NATURE REVIEWS MICROBIOLOGY

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

(2017) Teemu Kallonen et al.   GENOME RESEARCH

Genome-Wide Discovery of Genes Required for Capsule Production by Uropathogenic Escherichia coli

(2017) Kelvin G. K. Goh et al.   mBio

Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom

(2017) Hayley J. Brodrick et al.   Genome Medicine

Population structure ofEscherichia colicausing bacteraemia in the UK and Ireland between 2001 and 2010

(2016) M. J. Day et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences

(2016) Marie A. Chattaway et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

(2016) Roy M. Robins-Browne et al.   Frontiers in Cellular and Infection Microbiology

Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

(2016) Emily A. Pettengill et al.   Frontiers in Microbiology

Genomic diversity of EPEC associated with clinical presentations of differing severity

(2016) Tracy H. Hazen et al.   Nature Microbiology

Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants

(2016) Danielle J. Ingle et al.   Nature Microbiology

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource

(2015) Kate S. Baker et al.   Genome Medicine

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Large-scale genomic sequencing of extraintestinal pathogenicEscherichia colistrains

(2014) Stephen J. Salipante et al.   GENOME RESEARCH

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2014) Astrid von Mentzer et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Recent Advances in Understanding Enteric Pathogenic Escherichia coli

(2013) M. A. Croxen et al.   CLINICAL MICROBIOLOGY REVIEWS

Plasmids and the spread of resistance

(2013) Alessandra Carattoli   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study

(2013) Karen L Kotloff et al.   LANCET

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Refining the pathovar paradigm via phylogenomics of the attaching and effacing Escherichia coli

(2013) T. H. Hazen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Diversity and Fitness of E. coli Strains Recovered from the Intestinal and Urinary Tracts of Women with Recurrent Urinary Tract Infection

(2013) S. L. Chen et al.   Science Translational Medicine

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

(2012) Xavier Didelot et al.   BMC GENOMICS

Identification of acquired antimicrobial resistance genes

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

The ClermontEscherichia coliphylo-typing method revisited: improvement of specificity and detection of new phylo-groups

(2012) Olivier Clermont et al.   Environmental Microbiology Reports

Enterohemorrhagic E. coli (EHEC) pathogenesis

(2012) Y Nguyen et al.   Frontiers in Cellular and Infection Microbiology

Potential Pathogenicity and Host Range of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates from Healthy Poultry

(2011) Valeria Bortolaia et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance

(2011) A.-P. Magiorakos et al.   CLINICAL MICROBIOLOGY AND INFECTION

Enteropathogenic Escherichia coli infection in children

(2011) Theresa J. Ochoa et al.   CURRENT OPINION IN INFECTIOUS DISEASES

Animal and human pathogenic Escherichia coli strains share common genetic backgrounds

(2011) Olivier Clermont et al.   INFECTION GENETICS AND EVOLUTION

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

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

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

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY