Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones

One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock

(2019) Catherine Ludden et al.   mBio

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

(2019) Arun Gonzales Decano et al.   Scientific Reports

The Uropathogenic Escherichia coli Subclone ST131-H30 Is Responsible for Most Antibiotic Prescription Errors at an Urgent Care Clinic

(2018) Veronika Tchesnokova et al.   CLINICAL INFECTIOUS DISEASES

Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective

(2018) Jillian Rumore et al.   BMC GENOMICS

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

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

The Pandemic H30 Subclone of Sequence Type 131 (ST131) as the Leading Cause of Multidrug-Resistant Escherichia coli Infections in the United States (2011–2012)

(2017) James R. Johnson et al.   Open Forum Infectious Diseases

Escherichia coli and Staphylococcus aureus: bad news and good news from the European Antimicrobial Resistance Surveillance Network (EARS-Net, formerly EARSS), 2002 to 2009

(2017) C Gagliotti et al.   Eurosurveillance

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

Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131

(2016) Nouri L. Ben Zakour et al.   mBio

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

(2016) Nicole Stoesser et al.   mBio

Colonisation with ESBL-producing and carbapenemase-producing Enterobacteriaceae, vancomycin-resistant enterococci, and meticillin-resistant Staphylococcus aureus in a long-term care facility over one year

(2015) Catherine Ludden et al.   BMC INFECTIOUS DISEASES

Increasing Incidence of Extended-Spectrum β-Lactamase-Producing Escherichia coli in Community Hospitals throughout the Southeastern United States

(2015) Joshua T. Thaden et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

Application of Whole-Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology

(2015) Stephen J. Salipante et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Extraintestinal PathogenicEscherichia coli, a Common Human Pathogen: Challenges for Vaccine Development and Progress in the Field

(2015) Jan T. Poolman et al.   JOURNAL OF INFECTIOUS DISEASES

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system

(2015) Li-Yang Hsu et al.   GENOME BIOLOGY

Long-Term Care Facilities Are Reservoirs for Antimicrobial-Resistant Sequence Type 131 Escherichia coli

(2015) M. J. Burgess et al.   Open Forum Infectious Diseases

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

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

(2014) Astrid von Mentzer et al.   NATURE GENETICS

Global dissemination of a multidrug resistant Escherichia coli clone

(2014) N. K. Petty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Abrupt Emergence of a Single Dominant Multidrug-Resistant Strain of Escherichia coli

(2013) James R. Johnson et al.   JOURNAL OF INFECTIOUS DISEASES

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Different Factors Associated with CTX-M-Producing ST131 and Non-ST131 Escherichia coli Clinical Isolates

(2013) Marie-Hélène Nicolas-Chanoine et al.   PLoS One

The Epidemic of Extended-Spectrum- -Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone, H30-Rx

(2013) L. B. Price et al.   mBio

Clonal Composition and Community Clustering of Drug-Susceptible and -Resistant Escherichia coli Isolates from Bloodstream Infections

(2012) Sheila Adams-Sapper et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Effects of confounders and intermediates on the association of bacteraemia caused by extended-spectrum β-lactamase-producing Enterobacteriaceae and patient outcome: a meta-analysis

(2012) Wouter C. Rottier et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The revolving door between hospital and community: extended-spectrum beta-lactamase-producing Escherichia coli in Dublin

(2012) L. Burke et al.   JOURNAL OF HOSPITAL INFECTION

CTX-M Enzymes: Origin and Diffusion

(2012) Rafael Cantón et al.   Frontiers in Microbiology

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Costs of Bloodstream Infections Caused by Escherichia coli and Influence of Extended-Spectrum- -Lactamase Production and Inadequate Initial Antibiotic Therapy

(2010) M. Tumbarello et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

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

Faecal carriage of multidrug-resistant Gram-negative bacilli during a non-outbreak situation in a French university hospital

(2010) L. Vidal-Navarro et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain

(2010) B. A. Rogers et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

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

Context-driven discovery of gene cassettes in mobile integrons using a computational grammar

(2009) Guy Tsafnat et al.   BMC BIOINFORMATICS

Hospital and Societal Costs of Antimicrobial‐Resistant Infections in a Chicago Teaching Hospital: Implications for Antibiotic Stewardship

(2009) Rebecca R. Roberts et al.   CLINICAL INFECTIOUS DISEASES

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

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