Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation (Q34382739)

1 August 2017

title

Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation (English)

1 reference

1 August 2017

main subject

Staphylococcus aureus

1 reference

0 references

14

Andrew Rambaut

0 references

Davida S Smyth

Davida S Smyth

7

0 references

Adam A Witney

Adam Witney

11

0 references

Nouri L Ben Zakour

Nouri L Ben Zakour

2

0 references

Jodi A. Lindsay

Jodi A Lindsay

9

0 references

Jason Hinds

Jason Hinds

12

0 references

author name string

Caitriona M Guinane

1

1 reference

1 August 2017

Maria A Tormo-Mas

3

1 reference

1 August 2017

Lucy A Weinert

4

1 reference

1 August 2017

Bethan V Lowder

5

1 reference

1 August 2017

Robyn A Cartwright

6

1 reference

1 August 2017

Cyril J Smyth

8

1 reference

1 August 2017

Katherine A Gould

10

1 reference

1 August 2017

Jonathan P Bollback

13

1 reference

1 August 2017

José R Penadés

15

1 reference

1 August 2017

J Ross Fitzgerald

16

1 reference

1 August 2017

publication date

12 July 2010

1 reference

Genome Biology and Evolution

1 August 2017

published in

1 reference

1 August 2017

volume

2

1 reference

1 August 2017

page(s)

454-466

1 reference

Evolution of MRSA during hospital transmission and intercontinental spread

1 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Population structure of a hybrid clonal group of methicillin-resistant Staphylococcus aureus, ST239-MRSA-III.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Genetic requirements for Staphylococcus aureus abscess formation and persistence in host tissues

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Surface proteins that promote adherence of Staphylococcus aureus to human desquamated nasal epithelial cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Horizontal gene transfers link a human MRSA pathogen to contagious bovine mastitis bacteria

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Viewing and editing assembled sequences using Consed

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

The RAST Server: rapid annotations using subsystems technology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

BEAST: Bayesian evolutionary analysis by sampling trees

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Molecular correlates of host specialization in Staphylococcus aureus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Staphylococcal complement inhibitor: structure and active sites

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Genes under positive selection in Escherichia coli.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Living in a changing environment: insights into host adaptation in Neisseria meningitidis from comparative genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Characterization of Staphylococcus aureus isolates from buffalo, bovine, ovine, and caprine milk samples collected in Rio de Janeiro State, Brazil

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Characterization of the epidemic European fusidic acid-resistant impetigo clone of Staphylococcus aureus.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Predominance of clones carrying Panton-Valentine leukocidin genes among methicillin-resistant Staphylococcus aureus strains isolated in Japanese hospitals from 1979 to 1985.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Surface adhesins of Staphylococcus aureus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Host defenses against Staphylococcus aureus infection require recognition of bacterial lipoproteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Bacterial complement evasion.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Sau1: a novel lineage-specific type I restriction-modification system that blocks horizontal gene transfer into Staphylococcus aureus and between S. aureus isolates of different lineages

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Relaxed phylogenetics and dating with confidence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Microarrays reveal that each of the ten dominant lineages of Staphylococcus aureus has a unique combination of surface-associated and regulatory genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Evolutionary genetics of the accessory gene regulator (agr) locus in Staphylococcus aureus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Multilocus sequence typing of intercontinental bovine Staphylococcus aureus isolates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

ACT: the Artemis Comparison Tool

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Bayes empirical bayes inference of amino acid sites under positive selection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

HyPhy: hypothesis testing using phylogenies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Sorting a Staphylococcus aureus phage display library against ex vivo biomaterial

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Neutral mutations and neutral substitutions in bacterial genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Multilocus sequence typing of Staphylococcus aureus with DNA array technology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

How clonal is Staphylococcus aureus?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

A novel von Willebrand factor binding protein expressed by Staphylococcus aureus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Genome sequence survey identifies unique sequences and key virulence genes with unusual rates of amino Acid substitution in bovine Staphylococcus aureus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Genome and virulence determinants of high virulence community-acquired MRSA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Structural comparison of three types of staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Microbial genome analysis: insights into virulence, host adaptation and evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Artemis: sequence visualization and annotation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Characterization of a putative pathogenicity island from bovine Staphylococcus aureus encoding multiple superantigens

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Base-calling of automated sequencer traces using phred. I. Accuracy assessment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

PAML: a program package for phylogenetic analysis by maximum likelihood

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Vbeta-dependent stimulation of bovine and human T cells by host-specific staphylococcal enterotoxins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Molecular population genetic analysis of Staphylococcus aureus recovered from cows.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Role of Staphylococcus aureus coagulase and clumping factor in pathogenesis of experimental endocarditis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Effect of staphylococcal delta-toxin and bee venom peptide melittin on leukotriene induction and metabolism of human polymorphonuclear granulocytes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

A toxic shock syndrome toxin mutant of Staphylococcus aureus isolated by allelic replacement lacks virulence in a rabbit uterine model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Prophages of Staphylococcus aureus Newman and their contribution to virulence

6 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Heterogeneity among methicillin-resistant Staphylococcus aureus from Italian pig finishing holdings

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Gene replacement in Staphylococcus carnosus and Staphylococcus xylosus.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

The phylogeny of Staphylococcus aureus - which genes make the best intra-species markers?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Fine-structure molecular epidemiological analysis of Staphylococcus aureus recovered from cows

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Pathogenomic Analysis of the Common BovineStaphylococcus aureusClone (ET3): Emergence of a Virulent Subtype with Potential Risk to Public Health

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Enterotoxigenic Staphylococcus aureus in bulk milk in Norway

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Early expression of SCIN and CHIPS drives instant immune evasion by Staphylococcus aureus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Molecular genetic typing reveals further insights into the diversity of animal-associated Staphylococcus aureus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Staphylococcus aureus host specificity: comparative genomics of human versus animal isolates by multi-strain microarray

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Prophage, phiPV83-pro, carrying panton-valentine leukocidin genes, on the Staphylococcus aureus P83 chromosome: comparative analysis of the genome structures of phiPV83-pro, phiPVL, phi11, and other phages

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Inferring evolutionary trees with PAUP*.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2997551

Potential impact of recombination on sitewise approaches for detecting positive natural selection

27 October 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVQ031

Nucleotide Sequences and Biologic Properties of Toxic Shock Syndrome Toxin 1 from Ovine- and Bovine-Associated Staphylococcus aureus

21 January 2018

1 reference

12 December 2020

Delta-toxin from Staphylococcus aureus as a costimulator of human neutrophil oxidative burst

1 reference

12 December 2020

Comparison of Staphylococcus aureus recovered from personnel in a poultry hatchery and in broiler parent farms with those isolated from skeletal disease in broilers

1 reference

12 December 2020

A simplified system for biotyping Staphylococcus aureus strains isolated from different animal species

1 reference

12 December 2020

LukM/LukF'-PV is the most active Staphylococcus aureus leukotoxin on bovine neutrophils

1 reference

12 December 2020

Identifiers

DOI

10.1093/GBE/EVQ031

1 reference

1 August 2017

1 reference

1 August 2017

1 reference