(Q37554493)

21 August 2017

Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica (English)

1 reference

21 August 2017

0 references

whole genome sequencing

1 reference

based on heuristic

inferred from title

author

Frank Møller Aarestrup

5

Frank M Aarestrup

1 reference

PMC publication ID

3913712

Pimlapas Leekitcharoenphon

21 August 2017

Pimlapas Leekitcharoenphon

1

0 references

Rolf S. Kaas

Rolf S Kaas

3

0 references

Eva Møller Nielsen

Eva M Nielsen

2

0 references

Ole Lund

Ole Lund

4

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language of work or name

English

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publication date

4 February 2014

1 reference

21 August 2017

1 reference

21 August 2017

9

1 reference

21 August 2017

2

1 reference

21 August 2017

e87991

1 reference

Creative Commons Attribution 4.0 International

21 August 2017

start time

4 February 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

MUMmer

MUMmer

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

CMG-biotools, a free workbench for basic comparative microbial genomics.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

MLVA typing reveals higher genetic homogeneity among S. Enteritidis strains isolated from food, humans and chickens in Brazil in comparison to the North American strains.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

AGP: a multimethods web server for alignment-free genome phylogeny.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Nationwide outbreak of Salmonella Montevideo infections associated with contaminated imported black and red pepper: warehouse membership cards provide critical clues to identify the source

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Insights from genomics into bacterial pathogen populations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Routine use of microbial whole genome sequencing in diagnostic and public health microbiology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Transforming clinical microbiology with bacterial genome sequencing.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Genomic variation in Salmonella enterica core genes for epidemiological typing

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

High-resolution single nucleotide polymorphism analysis distinguishes recrudescence and reinfection in recurrent invasive nontyphoidal Salmonella typhimurium disease

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Multilocus sequence typing of total-genome-sequenced bacteria

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Characterization of isolates of Salmonella enterica serovar Stanley, a serovar endemic to Asia and associated with travel

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

The impact of recombination on dN/dS within recently emerged bacterial clones

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

The Salmonella enterica pan-genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Simrank: Rapid and sensitive general-purpose k-mer search tool

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Genomic characterization of Campylobacter jejuni strain M1.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

BEDTools: a flexible suite of utilities for comparing genomic features

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Evolution of MRSA during hospital transmission and intercontinental spread

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

The Sequence Alignment/Map format and SAMtools

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Fast and accurate short read alignment with Burrows-Wheeler transform

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Comparison of molecular typing methods for the differentiation of Salmonella foodborne pathogens

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Tandem repeat analysis for surveillance of human Salmonella Typhimurium infections

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Fast algorithms for large-scale genome alignment and comparison

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Nontyphoidal salmonellosis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Genome Sequences of Salmonella enterica Serovar Heidelberg Isolates Isolated in the United States from a Multistate Outbreak of Human Salmonella Infections

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Identification of acquired antimicrobial resistance genes

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Genome sequences of five Salmonella enterica serovar Heidelberg isolates associated with a 2011 multistate outbreak in the United States

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Standard operating procedure for computing pangenome trees

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Genomics of an emerging clone of Salmonella serovar Typhimurium ST313 from Nigeria and the Democratic Republic of Congo

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Segmented K-mer and its application on similarity analysis of mitochondrial genome sequences.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Molecular characterization of Salmonella Enteritidis: comparison of an optimized multi-locus variable-number of tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Molecular characterization of Salmonella Typhimurium highly successful outbreak strains.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

Salmonella enteritidis in Western Europe 1995-98 - a surveillance report from Enter-net.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3913712

10.1371/JOURNAL.PONE.0087991

1 September 2018

Identifiers

DOI

1 reference

21 August 2017

0 references

1 reference

PMC publication ID

3913712

21 August 2017

PubMed publication ID

24505344

1 reference

PMC publication ID

3913712