Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut

Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts

(2016) Andreas Porse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization

(2016) Sean Conlan et al.   mBio

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

(2016) Nicole Stoesser et al.   mBio

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

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

The gut microbiota and host health: a new clinical frontier

(2015) Julian R Marchesi et al.   GUT

A distributed cell division counter reveals growth dynamics in the gut microbiota

(2015) Cameron Myhrvold et al.   Nature Communications

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

Complete nucleotide sequence of pRS218, a large virulence plasmid, that augments pathogenic potential of meningitis-associated Escherichia coli strain RS218

(2014) Dona Saumya S Wijetunge et al.   BMC MICROBIOLOGY

The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach

(2014) Tom Vogwill et al.   Evolutionary Applications

Escherichia coli Isolate for Studying Colonization of the Mouse Intestine and Its Application to Two-Component Signaling Knockouts

(2014) M. Lasaro et al.   JOURNAL OF BACTERIOLOGY

Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions

(2014) Arun M. Nanda et al.   JOURNAL OF BACTERIOLOGY

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae

(2014) S. Conlan et al.   Science Translational Medicine

Genomic Diversity and Fitness of E. coli Strains Recovered from the Intestinal and Urinary Tracts of Women with Recurrent Urinary Tract Infection

(2013) S. L. Chen et al.   Science Translational Medicine

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

(2013) Christopher T Brown et al.   Microbiome

Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids

(2012) Bruce Humphrey et al.   BMC MICROBIOLOGY

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Easyfig: a genome comparison visualizer

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

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Mobilizable narrow host range plasmids as natural suicide vectors enabling horizontal gene transfer among distantly related bacterial species

(2011) Maria Smorawinska et al.   FEMS MICROBIOLOGY LETTERS

What defines extraintestinal pathogenic Escherichia coli?

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

Complete Genome Sequence of the Neonatal-Meningitis-Associated Escherichia coli Strain CE10

(2011) S. Lu et al.   JOURNAL OF BACTERIOLOGY

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

The stb Operon Balances the Requirements for Vegetative Stability and Conjugative Transfer of Plasmid R388

(2011) Catherine Guynet et al.   PLoS Genetics

Adaptation in a Mouse Colony Monoassociated with Escherichia coli K-12 for More than 1,000 Days

(2010) S. M. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

Pathogenicity-Associated Islands in Extraintestinal Pathogenic Escherichia coli Are Fitness Elements Involved in Intestinal Colonization

(2010) M. Diard et al.   JOURNAL OF BACTERIOLOGY

The epidemiology of urinary tract infection

(2010) Betsy Foxman   Nature Reviews Urology

Site-specific chromosomal integration of large synthetic constructs

(2010) Thomas E. Kuhlman et al.   NUCLEIC ACIDS RESEARCH

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

(2010) M. J. Morowitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human microbiome harbors a diverse reservoir of antibiotic resistance genes

(2010) Morten O.A. Sommer et al.   Virulence

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Use of fimH Single-Nucleotide Polymorphisms for Strain Typing of Clinical Isolates of Escherichia coli for Epidemiologic Investigation

(2009) R. C. S. Dias et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Pathogenomics of the Virulence Plasmids of Escherichia coli

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

Conjugative plasmids: vessels of the communal gene pool

(2009) A. Norman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2009) Chitrita DebRoy et al.   PLASMID

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Progress towards understanding the fate of plasmids in bacterial communities

(2008) Frances R. Slater et al.   FEMS MICROBIOLOGY ECOLOGY

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

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

Natural transfer of sulphonamide and ampicillin resistance between Escherichia coli residing in the human intestine

(2008) M. Trobos et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Nucleotide sequence of pOLA52: A conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux

(2008) Anders Norman et al.   PLASMID