An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates
Authors
Keywords
-
Journal
Scientific Reports
Volume 9, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2019-11-22
DOI
10.1038/s41598-019-54004-5
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
- Methodology for whole genome sequencing of MRSA in a routine hospital microbiology laboratory
- (2019) Kathy E. Raven et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Fast and flexible bacterial genomic epidemiology with PopPUNK
- (2019) John A. Lees et al. GENOME RESEARCH
- Whole-genome sequences of multidrug-resistant Escherichia coli in South-Kivu Province, Democratic Republic of Congo: characterization of phylogenomic changes, virulence and resistance genes
- (2019) Leonid M. Irenge et al. BMC INFECTIOUS DISEASES
- An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study
- (2019) Roan Pijnacker et al. LANCET INFECTIOUS DISEASES
- Fast hierarchical Bayesian analysis of population structure
- (2019) Gerry Tonkin-Hill et al. NUCLEIC ACIDS RESEARCH
- Two Health or Not Two Health? That Is the Question
- (2019) William P. Hanage mBio
- Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection
- (2019) Alan McNally et al. mBio
- Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size
- (2019) Sang-Cheol Park et al. Frontiers in Microbiology
- Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts
- (2019) Arun Gonzales Decano et al. mSphere
- Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 – tracking phylogenetic trajectories with Bayesian inference
- (2019) Sofia Ny et al. Scientific Reports
- Detection of OXA-48-like-producing Enterobacterales in Irish recreational water
- (2019) Bláthnaid M. Mahon et al. SCIENCE OF THE TOTAL ENVIRONMENT
- OUP accepted manuscript
- (2018) BIOINFORMATICS
- Automated annotation of mobile antibiotic resistance in Gram-negative bacteria: the Multiple Antibiotic Resistance Annotator (MARA) and database
- (2018) Sally R Partridge et al. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
- A genomic overview of the population structure of Salmonella
- (2018) Nabil-Fareed Alikhan et al. PLoS Genetics
- ST131 fimH22 Escherichia coli isolate with a blaCMY-2/IncI1/ST12 plasmid obtained from a patient with bloodstream infection: highly similar to E. coli isolates of broiler origin
- (2018) Louise Roer et al. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
- The European Nucleotide Archive in 2018
- (2018) Peter W Harrison et al. NUCLEIC ACIDS RESEARCH
- 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
- Fast and accurate de novo genome assembly from long uncorrected reads
- (2017) Robert Vaser et al. GENOME RESEARCH
- Evaluation of meat, fruit and vegetables from retail stores in five United Kingdom regions as sources of extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant Escherichia coli
- (2017) L.P. Randall et al. INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
- Global epidemiology of CTX-M β-lactamases: temporal and geographical shifts in genotype
- (2017) Edward R. Bevan et al. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
- 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
- Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
- (2017) Ryan R. Wick et al. PLoS Computational Biology
- Impact of extensive antibiotic treatment on faecal carriage of antibiotic-resistant enterobacteria in children in a low resistance prevalence setting
- (2017) Per Kristian Knudsen et al. PLoS One
- MultiQC: summarize analysis results for multiple tools and samples in a single report
- (2016) Philip Ewels et al. BIOINFORMATICS
- 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
- 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
- Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
- (2016) Alan McNally et al. PLoS Genetics
- Roary: rapid large-scale prokaryote pan genome analysis
- (2015) Andrew J. Page et al. BIOINFORMATICS
- The Role of Epidemic Resistance Plasmids and International High-Risk Clones in the Spread of Multidrug-Resistant Enterobacteriaceae
- (2015) Amy J. Mathers et al. CLINICAL MICROBIOLOGY REVIEWS
- The application of genomics to tracing bacterial pathogen transmission
- (2015) Nicholas J Croucher et al. CURRENT OPINION IN 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
- The role of pathogen genomics in assessing disease transmission
- (2015) V. Sintchenko et al. BMJ-British Medical Journal
- The role of pathogen genomics in assessing disease transmission
- (2015) V. Sintchenko et al. BMJ-British Medical Journal
- A New Clone Sweeps Clean: the Enigmatic Emergence of Escherichia coli Sequence Type 131
- (2014) Ritu Banerjee et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Prokka: rapid prokaryotic genome annotation
- (2014) T. Seemann BIOINFORMATICS
- 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
- Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
- (2014) Bruce J. Walker et al. PLoS One
- 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
- 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
- QUAST: quality assessment tool for genome assemblies
- (2013) Alexey Gurevich et al. BIOINFORMATICS
- BayesHammer: Bayesian clustering for error correction in single-cell sequencing
- (2013) Sergey I Nikolenko et al. BMC GENOMICS
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- 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
- Prevalent combination of virulence and plasmidic-encoded resistance in ST 131Escherichia colistrains
- (2013) Vera Calhau et al. Virulence
- The changing epidemiology of bacteraemias in Europe: trends from the European Antimicrobial Resistance Surveillance System
- (2012) M.E.A. de Kraker et al. CLINICAL MICROBIOLOGY AND INFECTION
- The presence of genes encoding for different virulence factors in clonally related Escherichia coli that produce CTX-Ms
- (2012) Akke K. Van der Bij et al. DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
- Role of Homologous Recombination in Adaptive Diversification of Extraintestinal Escherichia coli
- (2012) Sandip Paul et al. JOURNAL OF BACTERIOLOGY
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain
- (2012) K. A. Jolley et al. MICROBIOLOGY-SGM
- CTX-M Enzymes: Origin and Diffusion
- (2012) Rafael Cantón et al. Frontiers in Microbiology
- Characteristics of NDM-1-Producing Escherichia coli Isolates That Belong to the Successful and Virulent Clone ST131
- (2011) Gisele Peirano et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Easyfig: a genome comparison visualizer
- (2011) M. J. Sullivan et al. BIOINFORMATICS
- Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms
- (2011) Makrina Totsika et al. PLoS One
- Fast and accurate long-read alignment with Burrows–Wheeler transform
- (2010) Heng Li 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
- Comparative genomics: the bacterial pan-genome
- (2008) Hervé Tettelin et al. CURRENT OPINION IN MICROBIOLOGY
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started