Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

Molecular characterisation of Salmonella strains isolated from outbreaks and sporadic cases of diarrhoea occurred in Paraná State, South of Brazil

(2017) F. E. A. ASSIS et al.   EPIDEMIOLOGY AND INFECTION

Whole-Genome Comparative Analysis of Salmonella enterica Serovar Newport Strains Reveals Lineage-Specific Divergence

(2017) Jie Zheng et al.   Genome Biology and Evolution

Subtyping of Canadian isolates of Salmonella Enteritidis using Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) alone and in combination with Pulsed-Field Gel Electrophoresis (PFGE) and phage typing

(2017) Kim Ziebell et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Inflammation boosts bacteriophage transfer between Salmonella spp.

(2017) Médéric Diard et al.   SCIENCE

Does Sequence Conservation Provide Evidence for Biological Function?

(2017) Seila Omer et al.   TRENDS IN MICROBIOLOGY

Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa

(2017) Philip M. Ashton et al.   Genome Medicine

Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1

(2017) Siân V. Owen et al.   Frontiers in Microbiology

Bacteriophages Contribute to the Spread of Antibiotic Resistance Genes among Foodborne Pathogens of the Enterobacteriaceae Family – A Review

(2017) Anna Colavecchio et al.   Frontiers in Microbiology

Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity in Salmonella enterica

(2017) Anna Colavecchio et al.   Frontiers in Microbiology

A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis

(2017) Jean-Guillaume Emond-Rheault et al.   Frontiers in Microbiology

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

(2016) Nicholas A Feasey et al.   NATURE GENETICS

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease

(2016) Walid Mottawea et al.   Nature Communications

Identification ofSalmonellafor public health surveillance using whole genome sequencing

(2016) Philip M. Ashton et al.   PeerJ

Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations

(2015) S. Bekal et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa

(2015) Chinyere K. Okoro et al.   PLoS Neglected Tropical Diseases

Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

(2014) Evelien M. Adriaenssens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

(2014) David Coil et al.   BIOINFORMATICS

High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis

(2014) Dele Ogunremi et al.   BMC GENOMICS

Development of a New Molecular Subtyping Tool for Salmonella enterica Serovar Enteritidis Based on Single Nucleotide Polymorphism Genotyping Using PCR

(2014) D. Ogunremi et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Distribution of Gifsy-3 and of Variants of ST64B and Gifsy-1 Prophages amongst Salmonella enterica Serovar Typhimurium Isolates: Evidence that Combinations of Prophages Promote Clonality

(2014) Lester Hiley et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Inclusivity, exclusivity and limit of detection of commercially available real-time PCR assays for the detection of Salmonella

(2013) H. Margot et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the Evolutionary History, Population Genetics and Diversity among Isolates of Salmonella Enteritidis PFGE Pattern JEGX01.0004

(2013) Marc W. Allard et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa

(2012) Nicholas A Feasey et al.   LANCET

The Adaptation of Temperate Bacteriophages to Their Host Genomes

(2012) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Integrated Pipeline for de Novo Assembly of Microbial Genomes

(2012) Andrew Tritt et al.   PLoS One

The Salmonella enterica Pan-genome

(2011) Annika Jacobsen et al.   MICROBIAL ECOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

(2009) R. A. Kingsley et al.   GENOME RESEARCH

Identification of Salmonella using colony-print and detection with antibody-coated gold nanoparticles

(2009) Shiuh-Bin Fang et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

(2008) N. R. Thomson et al.   GENOME RESEARCH