SRST2: Rapid genomic surveillance for public health and hospital microbiology labs (Q34544298)

2 August 2017

title

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs (English)

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2 August 2017

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Harriet Dashnow

2

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Mark B. Schultz

object named as

Mark B Schultz

4

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Bernard Pope

object named as

Bernard J Pope

5

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Justin Zobel

7

object named as

Justin Zobel

1 reference

2 August 2017

1

Michael Inouye

1 reference

2 August 2017

Lesley-Ann Raven

3

1 reference

2 August 2017

Takehiro Tomita

6

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2 August 2017

Kathryn E Holt

8

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2 August 2017

publication date

20 November 2014

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2 August 2017

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2 August 2017

volume

6

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2 August 2017

issue

11

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2 August 2017

page(s)

90

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Creative Commons Attribution 4.0 International

2 August 2017

copyright license

start time

20 November 2014

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Live genomics for pathogen monitoring in public health.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Automated ensemble assembly and validation of microbial genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Deriving group A Streptococcus typing information from short-read whole-genome sequencing data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Genomic insights to control the emergence of vancomycin-resistant enterococci

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Rapid bacterial genome sequencing: methods and applications in clinical microbiology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Public health genomics and the new molecular epidemiology of bacterial pathogens

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Overview of molecular typing methods for outbreak detection and epidemiological surveillance.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Whole genome sequencing in the prevention and control of Staphylococcus aureus infection.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Transforming clinical microbiology with bacterial genome sequencing.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Short read sequence typing (SRST): multi-locus sequence types from short reads

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Identification of acquired antimicrobial resistance genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory--pipe dream or reality?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Fast gapped-read alignment with Bowtie 2

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Multilocus sequence typing of total-genome-sequenced bacteria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

GAGE: A critical evaluation of genome assemblies and assembly algorithms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Identification and correction of systematic error in high-throughput sequence data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Rapid Pneumococcal Evolution in Response to Clinical Interventions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Bacterial population genomics and infectious disease diagnostics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Coalescent simulation of intracodon recombination

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

The Sequence Alignment/Map format and SAMtools

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

A new perspective on Listeria monocytogenes evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Multilocus sequence typing of bacteria

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

How clonal is Staphylococcus aureus?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4237778

Identification of plasmids by PCR-based replicon typing

7 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/S13073-014-0090-6

Enterococcal vanB resistance locus in anaerobic bacteria in human faeces

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/S13073-014-0090-6

A sustained hospital outbreak of vancomycin-resistant Enterococcus faecium bacteremia due to emergence of vanB E. faecium sequence type 203.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/S13073-014-0090-6

10.1186/S13073-014-0090-6

21 January 2018

Identifiers

DOI

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Dimensions Publication ID

2 August 2017

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1 reference

2 August 2017

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