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

'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution

(2016) Alan McNally et al.   NATURE REVIEWS MICROBIOLOGY

The genomic signatures of Shigella evolution, adaptation and geographical spread

(2016) Hao Chung The et al.   NATURE REVIEWS MICROBIOLOGY

Loss of Multicellular Behavior in Epidemic African Nontyphoidal Salmonella enterica Serovar Typhimurium ST313 Strain D23580

(2016) Larissa A. Singletary et al.   mBio

Identification ofSalmonellafor public health surveillance using whole genome sequencing

(2016) Philip M. Ashton et al.   PeerJ

Ceftriaxone-Resistant Salmonella enterica Serotype Typhimurium Sequence Type 313 from Kenyan Patients Is Associated with theblaCTX-M-15Gene on a Novel IncHI2 Plasmid

(2015) Samuel Kariuki et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Multidrug Efflux Pumps from Enterobacteriaceae, Vibrio cholerae and Staphylococcus aureus Bacterial Food Pathogens

(2015) Jody Andersen et al.   International Journal of Environmental Research and Public Health

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

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

Characterization of the Invasive, Multidrug Resistant Non-typhoidal Salmonella Strain D23580 in a Murine Model of Infection

(2015) Jiseon Yang 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

Non-typhoidal Salmonella Typhimurium ST313 isolates that cause bacteremia in humans stimulate less inflammasome activation than ST19 isolates associated with gastroenteritis

(2015) Sarah Carden et al.   Pathogens and Disease

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Source Attribution of Human Salmonellosis: An Overview of Methods and Estimates

(2014) Sara M. Pires et al.   Foodborne Pathogens and Disease

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Identification of Novel Factors Involved in Modulating Motility of Salmonella enterica Serotype Typhimurium

(2014) Lydia M. Bogomolnaya et al.   PLoS One

Genomics of an emerging clone of Salmonella serovar Typhimurium ST313 from Nigeria and the Democratic Republic of Congo

(2013) Pimlapas Leekitcharoenphon et al.   Journal of Infection in Developing Countries

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

(2012) Michael Inouye et al.   BMC GENOMICS

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

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

(2012) Chinyere K Okoro et al.   NATURE GENETICS

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

(2012) Mark Achtman et al.   PLoS Pathogens

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genomes of the Most Dangerous Epidemic Bacteria Have a Virulence Repertoire Characterized by Fewer Genes but More Toxin-Antitoxin Modules

(2011) Kalliopi Georgiades et al.   PLoS One

Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly

(2011) Sherwood R. Casjens et al.   VIROLOGY

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   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

The porin OmpD from nontyphoidal Salmonella is a key target for a protective B1b cell antibody response

(2009) C. Gil-Cruz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage genomics

(2008) Graham F Hatfull   CURRENT OPINION IN MICROBIOLOGY