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

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Three Epidemics of Invasive Multidrug-ResistantSalmonellaBloodstream Infection in Blantyre, Malawi, 1998–2014

(2015) Nicholas A. Feasey et al.   CLINICAL INFECTIOUS DISEASES

Epidemiology and Genomics of Invasive NontyphoidalSalmonellaInfections in Kenya

(2015) Samuel Kariuki et al.   CLINICAL INFECTIOUS DISEASES

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

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

Reconstructing pathogen evolution from the ruins

(2015) Sean-Paul Nuccio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Modelling the Contributions of Malaria, HIV, Malnutrition and Rainfall to the Decline in Paediatric Invasive Non-typhoidal Salmonella Disease in Malawi

(2015) Nicholas A. Feasey et al.   PLoS Neglected Tropical Diseases

Invasive Salmonella Typhimurium ST313 with Naturally Attenuated Flagellin Elicits Reduced Inflammation and Replicates within Macrophages

(2015) Girish Ramachandran et al.   PLoS Neglected Tropical Diseases

Genetic Diversity and Evolution of Salmonella enterica Serovar Enteritidis Strains with Different Phage Types

(2014) J. Zheng et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Role of the st313-td Gene in Virulence of Salmonella Typhimurium ST313

(2014) Ana Herrero-Fresno et al.   PLoS One

Patterns of genome evolution that have accompanied host adaptation inSalmonella

(2014) Gemma C. Langridge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Analysis of Salmonella Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut

(2014) S.-P. Nuccio et al.   mBio

Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study

(2013) Karen L Kotloff et al.   LANCET

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng 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

Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar

(2013) R. A. Kingsley et al.   mBio

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection

(2013) Nicholas J. Croucher et al.   PLoS Genetics

Invasive Non-Typhoidal Salmonella Typhimurium ST313 Are Not Host-Restricted and Have an Invasive Phenotype in Experimentally Infected Chickens

(2013) Bryony N. Parsons et al.   PLoS Neglected Tropical Diseases

The "Decline and Fall" of Nontyphoidal Salmonella in the United Kingdom

(2012) S. J. O'Brien   CLINICAL INFECTIOUS DISEASES

Transposon Mutagenesis of Salmonella enterica Serovar Enteritidis Identifies Genes That Contribute to Invasiveness in Human and Chicken Cells and Survival in Egg Albumen

(2012) Devendra H. Shah et al.   INFECTION AND IMMUNITY

Identification of acquired antimicrobial resistance genes

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

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

(2012) Nicholas A Feasey et al.   LANCET

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

(2012) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

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

(2012) Chinyere K Okoro et al.   NATURE GENETICS

Salmonella Virchow isolates from human and avian origins in England - molecular characterization and infection of epithelial cells and poultry

(2011) A.-M. Salisbury et al.   JOURNAL OF APPLIED MICROBIOLOGY

PHAST: A Fast Phage Search Tool

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

Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota

(2011) P. Thiennimitr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Adaptation to the chicken intestine in Salmonella Enteritidis PT4 studied by transcriptional analysis

(2011) A.A. Dhawi et al.   VETERINARY MICROBIOLOGY

pUO-SeVR1 is an emergent virulence–resistance complex plasmid of Salmonella enterica serovar Enteritidis

(2010) I. Rodríguez et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Community-acquired bloodstream infections in Africa: a systematic review and meta-analysis

(2010) Elizabeth A Reddy et al.   LANCET INFECTIOUS DISEASES

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates

(2009) Laura Betancor et al.   BMC MICROBIOLOGY

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Salmonellosis Outcomes Differ Substantially by Serotype

(2008) Timothy F. Jones et al.   JOURNAL OF INFECTIOUS DISEASES

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS