The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales

An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study

(2019) Roan Pijnacker et al.   LANCET INFECTIOUS DISEASES

Real-Time PCR Assay for Differentiation of Typhoidal and Nontyphoidal Salmonella

(2019) Satheesh Nair et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SnapperDB: a database solution for routine sequencing analysis of bacterial isolates

(2018) Timothy Dallman et al.   BIOINFORMATICS

First Report of CTX-M-15 Salmonella Typhi From England

(2018) Gauri S Godbole et al.   CLINICAL INFECTIOUS DISEASES

Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012-2015

(2018) Sanch Kanagarajah et al.   FOOD MICROBIOLOGY

Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014

(2018) Alison Waldram et al.   FOOD MICROBIOLOGY

Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak

(2018) Madison E. Pearce et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

A genomic overview of the population structure of Salmonella

(2018) Nabil-Fareed Alikhan et al.   PLoS Genetics

Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica

(2018) Saskia Neuert et al.   Frontiers in Microbiology

Evaluation of whole genome sequencing for the identification and typing of Vibrio cholerae

(2018) David R. Greig et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal Salmonella

(2018) Marcus Nguyen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Utility of Whole Genome Sequencing To Describe the Persistence and Evolution of Listeria monocytogenes Strains within Crabmeat Processing Environments Linked to Two Outbreaks of Listeriosis

(2018) RICHARD ELSON et al.   JOURNAL OF FOOD PROTECTION

First use of whole-genome sequencing to investigate a cluster of Yersinia enterocolitica, Liverpool, United Kingdom, 2017

(2018) Thomas Inns et al.   JOURNAL OF MEDICAL MICROBIOLOGY

PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

(2017) Celine Nadon et al.   Eurosurveillance

Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi

(2017) Martin R Day et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife

(2017) Milton Thomas et al.   Gut Pathogens

Whole-Genome Sequencing for National Surveillance of Shigella flexneri

(2017) Marie A. Chattaway et al.   Frontiers in Microbiology

Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis

(2016) T. INNS et al.   EPIDEMIOLOGY AND INFECTION

WGS for surveillance of antimicrobial resistance: a pilot study to detect the prevalence and mechanism of resistance to azithromycin in a UK population of non-typhoidalSalmonella

(2016) Satheesh Nair et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Detection of the plasmid-mediatedmcr-1gene conferring colistin resistance in human and food isolates ofSalmonella entericaandEscherichia coliin England and Wales

(2016) Michel Doumith et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences

(2016) Marie A. Chattaway et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Detection of Infectious Disease Outbreaks From Laboratory Data With Reporting Delays

(2016) Angela Noufaily et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Whole Genome Sequencing for Public Health Surveillance of Shiga Toxin-Producing Escherichia coli Other than Serogroup O157

(2016) Marie A. Chattaway et al.   Frontiers in Microbiology

MOST: a modified MLST typing tool based on short read sequencing

(2016) Rediat Tewolde et al.   PeerJ

Identification ofSalmonellafor public health surveillance using whole genome sequencing

(2016) Philip M. Ashton et al.   PeerJ

The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

(2016) Catherine E. Yoshida et al.   PLoS One

A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: ‘near real-time’ application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2014

(2015) T Inns et al.   Eurosurveillance

Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

(2015) Erika Scaltriti et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

(2015) Angela J. Taylor et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data

(2015) Shaokang Zhang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

Rapid identification of Salmonella enterica subsp. arizonae and S. enterica subsp. diarizonae by real-time polymerase chain reaction

(2009) Katie L. Hopkins et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Supplement 2003–2007 (No. 47) to the White-Kauffmann-Le Minor scheme

(2009) Martine Guibourdenche et al.   RESEARCH IN MICROBIOLOGY