Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

Fast and flexible bacterial genomic epidemiology with PopPUNK

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

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome

(2018) Taj Azarian et al.   PLoS Pathogens

PANINI: Pangenome Neighbour Identification for Bacterial Populations

(2018) Khalil Abudahab et al.   Microbial 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

Import and spread of extended-spectrum β-lactamase-producing Enterobacteriaceae by international travellers (COMBAT study): a prospective, multicentre cohort study

(2017) Maris S Arcilla et al.   LANCET INFECTIOUS DISEASES

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage

(2017) Sonja Lehtinen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics

(2017) Jukka Corander et al.   Nature Ecology & Evolution

Prolonged colonisation withEscherichia coliO25:ST131 versus other extended-spectrum beta-lactamase-producingE. coliin a long-term care facility with high endemic level of rectal colonisation, the Netherlands, 2013 to 2014

(2016) Ilse Overdevest et al.   Eurosurveillance

'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution

(2016) Alan McNally et al.   NATURE REVIEWS MICROBIOLOGY

Siderophore vaccine conjugates protect against uropathogenicEscherichia coliurinary tract infection

(2016) Laura A. Mike et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

The cytochrome bd-I respiratory oxidase augments survival of multidrug-resistant Escherichia coli during infection

(2016) Mark Shepherd et al.   Scientific Reports

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

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

Comparative genome analysis identifies few traits unique to the Escherichia coli ST131 H30Rx clade and extensive mosaicism at the capsule locus

(2014) Abdulaziz Alqasim et al.   BMC GENOMICS

Large-scale genomic sequencing of extraintestinal pathogenicEscherichia colistrains

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

AcrB, AcrD, and MdtABC Multidrug Efflux Systems Are Involved in Enterobactin Export in Escherichia coli

(2014) Tsukasa Horiyama 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

Host-specific induction ofEscherichia colifitness genes during human urinary tract infection

(2014) Sargurunathan Subashchandrabose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversification of bacterial genome content through distinct mechanisms over different timescales

(2014) Nicholas J. Croucher et al.   Nature Communications

The Evolutionary Path to Extraintestinal Pathogenic, Drug-Resistant Escherichia coli Is Marked by Drastic Reduction in Detectable Recombination within the Core Genome

(2013) Alan McNally et al.   Genome 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

Combining Quantitative Genetic Footprinting and Trait Enrichment Analysis to Identify Fitness Determinants of a Bacterial Pathogen

(2013) Travis J. Wiles et al.   PLoS Genetics

Genome-Wide Detection of Fitness Genes in Uropathogenic Escherichia coli during Systemic Infection

(2013) Sargurunathan Subashchandrabose et al.   PLoS Pathogens

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

(2012) S. Kumar et al.   BIOINFORMATICS

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

Genomic analysis uncovers a phenotypically diverse but genetically homogeneous Escherichia coli ST131 clone circulating in unrelated urinary tract infections

(2012) G. Clark et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

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

Genomic fluidity: an integrative view of gene diversity within microbial populations

(2011) Andrey O Kislyuk et al.   BMC GENOMICS

What defines extraintestinal pathogenic Escherichia coli?

(2011) Christian-Daniel Köhler et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Molecular epidemiology of extraintestinal pathogenic Escherichia coli isolates from a regional cohort of elderly patients highlights the prevalence of ST131 strains with increased antimicrobial resistance in both community and hospital care settings

(2011) G. Croxall et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Gut inflammation provides a respiratory electron acceptor for Salmonella

(2010) Sebastian E. Winter et al.   NATURE

The epidemiology of urinary tract infection

(2010) Betsy Foxman   Nature Reviews Urology

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

(2008) Jukka Corander et al.   BMC BIOINFORMATICS

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

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

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