Phylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group

Rapid and Extensive Expansion in the U.S. of a New Multidrug-Resistant Escherichia coli Clonal Group, Sequence Type ST1193

(2018) Veronika L Tchesnokova et al.   CLINICAL INFECTIOUS DISEASES

Prevalence of ESBL/AmpC genes and specific clones among the third-generation cephalosporin-resistant Enterobacteriaceae from canine and feline clinical specimens in Japan

(2018) Yoshihiko Maeyama et al.   VETERINARY MICROBIOLOGY

A genomic overview of the population structure of Salmonella

(2018) Nabil-Fareed Alikhan et al.   PLoS Genetics

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

(2018) Zhemin Zhou et al.   GENOME RESEARCH

Molecular Characteristics of ST1193 Clone among Phylogenetic Group B2 Non-ST131 Fluoroquinolone-Resistant Escherichia coli

(2017) Jing Wu et al.   Frontiers in Microbiology

Prevalence of ST1193 clone and IncI1/ST16 plasmid in E-coli isolates carrying blaCTX-M-55 gene from urinary tract infections patients in China

(2017) Liang Xia et al.   Scientific Reports

tipdatingbeast : an r package to assist the implementation of phylogenetic tip-dating tests using beast

(2016) Adrien Rieux et al.   Molecular Ecology Resources

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

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

(2016) Nicole Stoesser et al.   mBio

Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids

(2016) Tatiana Dimitriu et al.   PLOS BIOLOGY

Lethal neonatal meningoencephalitis caused by multi-drug resistant, highly virulentEscherichia coli

(2016) Junaid Iqbal et al.   Infectious Diseases

Separate F-Type Plasmids Have Shaped the Evolution of the H 30 Subclone of Escherichia coli Sequence Type 131

(2016) Timothy J. Johnson et al.   mSphere

The Niche forEscherichia coliSequence Type 131 Among Veterans: Urinary Tract Abnormalities and Long-Term Care Facilities

(2016) Dimitri M. Drekonja et al.   Open Forum Infectious Diseases

Variation in Resistance Traits, Phylogenetic Backgrounds, and Virulence Genotypes among Escherichia coli Clinical Isolates from Adjacent Hospital Campuses Serving Distinct Patient Populations

(2015) Sarah M. Drawz et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes

(2015) Olivier Clermont et al.   MICROBIOLOGY-SGM

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Molecular Epidemiology and Genetic Diversity of Fluoroquinolone-Resistant Escherichia coli Isolates from Patients with Community-Onset Infections in 30 Chinese County Hospitals

(2014) Lina Zhao et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Prevalence and characteristics of lactose non-fermenting Escherichia coli in urinary isolates

(2014) Jiyoung Chang et al.   JOURNAL OF INFECTION AND CHEMOTHERAPY

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

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

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

Escherichia coli Sequence Type 131 (ST131) Subclone H30 as an Emergent Multidrug-Resistant Pathogen Among US Veterans

(2013) Aylin Colpan et al.   CLINICAL INFECTIOUS DISEASES

Escherichia coli Sequence Type 131 Is a Dominant, Antimicrobial-Resistant Clonal Group Associated with Healthcare and Elderly Hosts

(2013) Ritu Banerjee et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

Detection of clonally related Escherichia coli isolates producing different CMY β-lactamases from a cystic fibrosis patient

(2013) Lise Crémet et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Prominence of an O75 Clonal Group (Clonal Complex 14) among Non-ST131 Fluoroquinolone-Resistant Escherichia coli Causing Extraintestinal Infections in Humans and Dogs in Australia

(2012) Joanne L. Platell et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari 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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Virulence Plasmid Harbored by Uropathogenic Escherichia coli Functions in Acute Stages of Pathogenesis

(2010) C. K. Cusumano et al.   INFECTION AND IMMUNITY

Pathogenomics of the Virulence Plasmids of Escherichia coli

(2009) T. J. Johnson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Complete sequence of pEC14_114, a highly conserved IncFIB/FIIA plasmid associated with uropathogenic Escherichia coli cystitis strains

(2009) Chitrita DebRoy et al.   PLASMID

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

(2009) Marie Touchon et al.   PLoS Genetics