Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains (Q35049379)

6 August 2017

title

Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains (English)

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Extraintestinal Pathogenic Escherichia coli

6 August 2017

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9

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6 August 2017

6

Susan M Butler-Wu

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6 August 2017

Stephen J Salipante

1

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6 August 2017

David J Roach

2

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6 August 2017

Jacob O Kitzman

3

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6 August 2017

Matthew W Snyder

4

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6 August 2017

Bethany Stackhouse

5

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6 August 2017

Choli Lee

7

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6 August 2017

Brad T Cookson

8

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6 August 2017

publication date

4 November 2014

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6 August 2017

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6 August 2017

volume

25

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6 August 2017

issue

1

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6 August 2017

page(s)

119-128

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Whole-genome sequencing for high-resolution investigation of methicillin-resistant Staphylococcus aureus epidemiology and genome plasticity

6 August 2017

cites work

1 reference

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Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association.

8 July 2018

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Predicting the virulence of MRSA from its genome sequence

8 July 2018

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Characterization of Escherichia coli isolates from hospital inpatients or outpatients with urinary tract infection

8 July 2018

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Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone

8 July 2018

1 reference

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Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States

8 July 2018

1 reference

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The epidemic of extended-spectrum-β-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx

8 July 2018

1 reference

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An Unusual Case of Early Onset Persistent Escherichia coli Septicemia Associated with Endocarditis

8 July 2018

1 reference

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Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

8 July 2018

1 reference

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Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Escherichia coli sequence type 131 (ST131) subclone H30 as an emergent multidrug-resistant pathogen among US veterans

8 July 2018

1 reference

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Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Evolution of Staphylococcus aureus and MRSA during outbreaks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Leukemia and risk of recurrent Escherichia coli bacteremia: genotyping implicates E. coli translocation from the colon to the bloodstream.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

The rise of a digital immune system

8 July 2018

1 reference

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Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Clonal composition and community clustering of drug-susceptible and -resistant Escherichia coli isolates from bloodstream infections

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Escherichia coli isolates that carry vat, fyuA, chuA, and yfcV efficiently colonize the urinary tract

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Transforming clinical microbiology with bacterial genome sequencing.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Transmission dynamics of extended-spectrum β-lactamase-producing Enterobacteriaceae in the tertiary care hospital and the household setting

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Population structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli from Northwest England.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Statistics and truth in phylogenomics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

PHAST: a fast phage search tool

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

The origin of the Haitian cholera outbreak strain

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Complete nucleotide sequence analysis of plasmids in strains of Staphylococcus aureus clone USA300 reveals a high level of identity among isolates with closely related core genome sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Distribution and evolution of virulence factors in septicemic Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

FastTree 2--approximately maximum-likelihood trees for large alignments

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Genome evolution and adaptation in a long-term experiment with Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

The Sequence Alignment/Map format and SAMtools

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Fast and accurate short read alignment with Burrows-Wheeler transform

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

ABySS: a parallel assembler for short read sequence data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Mechanisms accounting for fluoroquinolone resistance in Escherichia coli clinical isolates

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Endemic and epidemic lineages of Escherichia coli that cause urinary tract infections

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Identifying bacterial genes and endosymbiont DNA with Glimmer

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Principal components analysis corrects for stratification in genome-wide association studies

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Enhanced persistence in the colonic microbiota of Escherichia coli strains belonging to phylogenetic group B2: role of virulence factors and adherence to colonic cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Analysis of a uropathogenic Escherichia coli clonal group by multilocus sequence typing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Phylogenomics and the reconstruction of the tree of life

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Identification and characterization of a novel uropathogenic Escherichia coli-associated fimbrial gene cluster

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Pathogenic Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

The epidemiology of sepsis in the United States from 1979 through 2000

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Rapid and simple determination of the Escherichia coli phylogenetic group

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Analysis of the F antigen-specific papA alleles of extraintestinal pathogenic Escherichia coli using a novel multiplex PCR-based assay

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

The link between phylogeny and virulence in Escherichia coli extraintestinal infection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Escherichia coli molecular phylogeny using the incongruence length difference test

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Transmission of uropathogens between sex partners

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Basic local alignment search tool

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

DNA sequences of three papA genes from uropathogenic Escherichia coli strains: evidence of structural and serological conservation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Association of carboxylesterase B electrophoretic pattern with presence and expression of urovirulence factor determinants and antimicrobial resistance among strains of Escherichia coli that cause urosepsis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4317167

Identification of forces shaping the commensal Escherichia coli genetic structure by comparing animal and human isolates.

8 July 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.180190.114

Genome-wide association mapping in bacteria?

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.180190.114

Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.180190.114

Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.180190.114

Escherichia coli colonization patterns among human household members and pets, with attention to acute urinary tract infection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.180190.114

Multidrug-resistant Escherichia coli clonal groups causing community-acquired pyelonephritis

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.180190.114

Virulence factor profiles and phylogenetic background of Escherichia coli isolates from veterans with bacteremia and uninfected control subjects

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.180190.114

Prevalence of enterotoxins among Escherichia coli isolates causing bacteraemia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.180190.114

Localization of the receptor-binding protein adhesin at the tip of the bacterial pilus

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.180190.114

Long-term carriage of extended-spectrum beta-lactamase-producing Escherichia coli

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25373147

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.180190.114

1 reference

6 August 2017

1 reference

6 August 2017

1 reference