Specificities and Commonalities of Carbapenemase-Producing Escherichia coli Isolated in France from 2012 to 2015

Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients

(2021) Ricardo León-Sampedro et al.   Nature Microbiology

bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands

(2021) Antoni P. A. Hendrickx et al.   Microbial Genomics

Molecular characteristics of carbapenemase-producing Enterobacterales in the Netherlands; results of the 2014-2018 national laboratory surveillance

(2020) Kim van der Zwaluw et al.   CLINICAL MICROBIOLOGY AND INFECTION

Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli

(2020) Rafael Patiño-Navarrete et al.   Genome Medicine

Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community

(2020) Yusuke Matsui et al.   MicrobiologyOpen

ResFinder 4.0 for predictions of phenotypes from genotypes

(2020) Valeria Bortolaia et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The Gut of Healthy Infants in the Community as a Reservoir of ESBL and Carbapenemase-Producing Bacteria

(2020) Ali F. Saleem et al.   Antibiotics-Basel

Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae

(2020) Sophia David et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

(2019) Sophia David et al.   Nature Microbiology

Emergence of diversity in carbapenemase-producing Escherichia coli ST131, England, January 2014 to June 2016

(2019) Nicholas Ellaby et al.   Eurosurveillance

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

(2019) Arun Gonzales Decano et al.   Scientific Reports

Diversity of carbapenemase-producing Escherichia coli isolates, France 2012-2013

(2018) Lauraine Gauthier et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario

(2018) Laura Becker et al.   Frontiers in Microbiology

Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones

(2018) Louise Roer et al.   mSphere

Analysis of OXA-204 carbapenemase-producing Enterobacteriaceae reveals possible endoscopy-associated transmission, France, 2012 to 2014

(2017) Anaïs Potron et al.   Eurosurveillance

Trends in carbapenemase-producing Enterobacteriaceae, France, 2012 to 2014

(2017) Laurent Dortet et al.   Eurosurveillance

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study

(2017) Hajo Grundmann et al.   LANCET INFECTIOUS DISEASES

Atropos: specific, sensitive, and speedy trimming of sequencing reads

(2017) John P. Didion et al.   PeerJ

Carbapenemase-producingEscherichia coliis becoming more prevalent in Spain mainly because of the polyclonal dissemination of OXA-48

(2016) Adriana Ortega et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Clonal expansion of Escherichia coli ST38 carrying a chromosomally integrated OXA-48 carbapenemase gene

(2016) Jane F. Turton et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Phylogenetic, virulence and antibiotic resistance characteristics of commensal strain populations of Escherichia coli from community subjects in the Paris area in 2010 and evolution over 30 years

(2016) Méril Massot et al.   MICROBIOLOGY-SGM

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

(2016) Nicole Stoesser et al.   mBio

French recommendations for the prevention of ‘emerging extensively drug-resistant bacteria’ (eXDR) cross-transmission

(2015) D. Lepelletier et al.   JOURNAL OF HOSPITAL INFECTION

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

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Escherichia coli ST131, an Intriguing Clonal Group

(2014) M.-H. Nicolas-Chanoine et al.   CLINICAL MICROBIOLOGY REVIEWS

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

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

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

(2014) Jason W. Sahl et al.   PeerJ

Derepressed Transfer Properties Leading to the Efficient Spread of the Plasmid Encoding Carbapenemase OXA-48

(2013) Anaïs Potron et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

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

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

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

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

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains

(2011) M.A. Leverstein-van Hall et al.   CLINICAL MICROBIOLOGY AND INFECTION

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Updated Functional Classification of  -Lactamases

(2009) K. Bush et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Extended-spectrum β-lactamase-producing Escherichia coli in Spain belong to a large variety of multilocus sequence typing types, including ST10 complex/A, ST23 complex/A and ST131/B2

(2009) Jesús Oteo et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

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

(2009) Marie Touchon et al.   PLoS Genetics