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Revolutionising Public Health Reference Microbiology using Whole Genome Sequencing: Salmonella as an exemplar
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1001/jamainternmed.2013.7734openalex-snapshot
Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology
inferredcites →https://doi.org/10.1002/sim.5595openalex-snapshot
An improved algorithm for outbreak detection in multiple surveillance systems
inferredcites →https://doi.org/10.1007/978-1-60327-999-4_6openalex-snapshot
Pulsed-Field Gel Electrophoresis for Molecular Epidemiology of Food Pathogens
inferredcites →https://doi.org/10.1016/j.diagmicrobio.2011.01.015openalex-snapshot
A novel real-time polymerase chain reaction for identification of Salmonella enterica subspecies enterica
inferredcites →https://doi.org/10.1017/s0022172400020209openalex-snapshot
A new phage-typing scheme forSalmonella typhi-murium
inferredcites →https://doi.org/10.1038/nbt.2198openalex-snapshot
Performance comparison of benchtop high-throughput sequencing platforms
inferredcites →https://doi.org/10.1038/ng.195openalex-snapshot
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/nrmicro1901openalex-snapshot
Microbiology in the post-genomic era
inferredcites →https://doi.org/10.1056/nejmc1100443openalex-snapshot
Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1099/jmm.0.072702-0openalex-snapshot
Salmonella enterica subspecies II infections in England and Wales – the use of multilocus sequence typing to assist serovar identification
inferredcites →https://doi.org/10.1128/jcm.03617-13openalex-snapshot
Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli
inferredcites →https://doi.org/10.1186/1471-2164-13-338openalex-snapshot
Short read sequence typing (SRST): multi-locus sequence types from short reads
inferredcites →https://doi.org/10.1186/s13059-014-0572-2openalex-snapshot
De novo assembly of bacterial transcriptomes from RNA-seq data
inferredcites →https://doi.org/10.1371/currents.outbreaks.2c05a47d292f376afc5a6fcdd8a7a3b6openalex-snapshot
Whole Genome Sequencing for the Retrospective Investigation of an Outbreak of Salmonella Typhimurium DT 8
inferredcites →https://doi.org/10.1371/journal.ppat.1002776openalex-snapshot
Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica
inferredcites →https://doi.org/10.1371/journal.ppat.1002824openalex-snapshot
Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology
inferredcites →https://doi.org/10.2807/1560-7917.es2014.19.31.20866openalex-snapshot
A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012
inferredcites →https://doi.org/10.2807/ese.16.32.19942-enopenalex-snapshot
Standardisation of multilocus variable-number tandem-repeat analysis (MLVA) for subtyping of Salmonella enterica serovar Enteritidis
inferredcites →https://doi.org/10.3201/eid2008.131399openalex-snapshot
Rapid Whole-Genome Sequencing for Surveillance ofSalmonella entericaSerovar Enteritidis
inferredcites →https://doi.org/10.3390/pathogens3010093openalex-snapshot
Live Genomics for Pathogen Monitoring in Public Health
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/978-3-030-62155-1_5openalex-snapshot
Epidemiological Typing Using WGS
inferred← citeshttps://doi.org/10.1007/978-3-030-85877-3_7-1openalex-snapshot
Zoonoses in Food-Chain Animals with Respect to Human Disease and Public Health Relevance
inferred← citeshttps://doi.org/10.1007/978-3-031-27164-9_7openalex-snapshot
The Zoonotic Agent Salmonella
inferred← citeshttps://doi.org/10.1007/s00217-019-03423-9openalex-snapshot
Immuno- and nucleic acid-based current technique for Salmonella detection in food
inferred← citeshttps://doi.org/10.1007/s10096-016-2591-2openalex-snapshot
Comparative study of all Salmonella enterica serovar Enteritidis strains isolated from food and food animals in Greece from 2008 to 2010 with clinical isolates
inferred← citeshttps://doi.org/10.1016/j.fm.2017.02.012openalex-snapshot
Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014
inferred← citeshttps://doi.org/10.1016/j.fm.2017.08.017openalex-snapshot
Evaluation of WGS based approaches for investigating a food-borne outbreak caused by Salmonella enterica serovar Derby in Germany
inferred← citeshttps://doi.org/10.1016/j.ijfoodmicro.2018.02.023openalex-snapshot
Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak
inferred← citeshttps://doi.org/10.1016/j.micinf.2016.10.009openalex-snapshot
1926–2016: 90 Years of listeriology
inferred← citeshttps://doi.org/10.1016/j.tim.2016.02.004openalex-snapshot
Divorcing Strain Classification from Species Names
inferred← citeshttps://doi.org/10.1016/j.ygeno.2019.02.016openalex-snapshot
A proposed core genome scheme for analyses of the Salmonella genus
inferred← citeshttps://doi.org/10.1017/s0950268816001941openalex-snapshot
Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak ofSalmonellaEnteritidis
inferred← citeshttps://doi.org/10.1017/s0950268817002953openalex-snapshot
Online market research panel members as controls in case–control studies to investigate gastrointestinal disease outbreaks: early experiences and lessons learnt from the UK
inferred← citeshttps://doi.org/10.1017/s0950268818001589openalex-snapshot
Operational burden of implementing Salmonella Enteritidis and Typhimurium cluster detection using whole genome sequencing surveillance data in England: a retrospective assessment
inferred← citeshttps://doi.org/10.1038/ng.3644openalex-snapshot
Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings
inferred← citeshttps://doi.org/10.1038/s41564-020-00836-1openalex-snapshot
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
inferred← citeshttps://doi.org/10.1099/mgen.0.000070openalex-snapshot
Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network
inferred← citeshttps://doi.org/10.1099/mgen.0.000318openalex-snapshot
Concordance of SNP- and allele-based typing workflows in the context of a large-scale international Salmonella Enteritidis outbreak investigation
inferred← citeshttps://doi.org/10.1099/mgen.0.000605openalex-snapshot
Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing
inferred← citeshttps://doi.org/10.1101/2020.06.30.169953openalex-snapshot
Elucidation of global and local genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing
inferred← citeshttps://doi.org/10.1128/jcm.00119-18openalex-snapshot
Whole-Genome Sequencing of Recent Listeria monocytogenes Isolates from Germany Reveals Population Structure and Disease Clusters
inferred← citeshttps://doi.org/10.11606/t.42.2018.tde-23022018-114716openalex-snapshot
Identificação e caracterização de bactérias patogênicas e indicadoras por métodos de cultivo e moleculares.
inferred← citeshttps://doi.org/10.1186/s13073-015-0254-zopenalex-snapshot
Moving pathogen genomics out of the lab and into the clinic: what will it take?
inferred← citeshttps://doi.org/10.1371/journal.pntd.0007485openalex-snapshot
Emergence of phylogenetically diverse and fluoroquinolone resistant Salmonella Enteritidis as a cause of invasive nontyphoidal Salmonella disease in Ghana
inferred← citeshttps://doi.org/10.21203/rs.3.rs-10120722/v1openalex-snapshot
Whole-genome investigations of Salmonella enterica isolates from poultry meat uncovered multidrug-resistant and outbreak-associated serovars circulating in Accra, Ghana
inferred← citeshttps://doi.org/10.2807/1560-7917.es.2017.22.49.17-00037openalex-snapshot
Investigation using whole genome sequencing of a prolonged restaurant outbreak of Salmonella Typhimurium linked to the building drainage system, England, February 2015 to March 2016
inferred← citeshttps://doi.org/10.2807/1560-7917.es.2020.25.20.1900519openalex-snapshot
Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens
inferred← citeshttps://doi.org/10.2903/sp.efsa.2017.en-1188openalex-snapshot
Multi‐country outbreak of Salmonella Enteritidis phage type 8, MLVA profile 2‐9‐7‐3‐2 and 2‐9‐6‐3‐2 infections
inferred← citeshttps://doi.org/10.2903/sp.efsa.2017.en-1353openalex-snapshot
Multi‐country outbreak of Salmonella Enteritidis infections linked to Polish eggs
inferred← citeshttps://doi.org/10.2903/sp.efsa.2018.en-1465openalex-snapshot
Multi‐country outbreak of Salmonella Agona infections possibly linked to ready‐to‐eat food
inferred← citeshttps://doi.org/10.2903/sp.efsa.2020.en-1799openalex-snapshot
Multi‐country outbreak of Salmonella Enteritidis infections linked to eggs, third update – 6 February 2020
inferred← citeshttps://doi.org/10.3201/eid2211.160653openalex-snapshot
ESBL-Producing and Macrolide-Resistant Shigella sonnei Infections among Men Who Have Sex with Men, England, 2015
inferred← citeshttps://doi.org/10.3389/fmicb.2019.00144openalex-snapshot
Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges
inferred← citeshttps://doi.org/10.3389/fmicb.2019.02897openalex-snapshot
Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept
inferred← citeshttps://doi.org/10.3389/fmicb.2021.752883openalex-snapshot
Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019
inferred← citeshttps://doi.org/10.3389/fmicb.2026.1746150openalex-snapshot
Comparative genomic and ecological insights into Salmonella enterica serovar Kumasi ST2302 from the first Asian clinical isolate
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