Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa

Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice

(2020) Bidong D. Nguyen et al.   Cell Host & Microbe

Invasive non-typhoidal Salmonella infections in sub-Saharan Africa: a systematic review on antimicrobial resistance and treatment

(2020) Bieke Tack et al.   BMC Medicine

Investigating the meat pathway as a source of human nontyphoidal Salmonella bloodstream infections and diarrhea in East Africa

(2020) John A Crump et al.   CLINICAL INFECTIOUS DISEASES

Pathogenic signature of invasive non-typhoidal Salmonella in Africa: implications for vaccine development

(2020) Giulia Piccini et al.   Human Vaccines & Immunotherapeutics

Genetic variation in the MacAB-TolC efflux pump influences pathogenesis of invasive Salmonella isolates from Africa

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Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580

(2019) Rocío Canals et al.   PLOS BIOLOGY

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Salmonella Panama: An understudied serovar responsible for extra-intestinal salmonellosis worldwide

(2019) Caisey V. Pulford et al.   INFECTION AND IMMUNITY

Parallel evolution leading to impaired biofilm formation in invasive Salmonella strains

(2019) Keith D. MacKenzie et al.   PLoS Genetics

Genomic analysis of human invasive Salmonella enterica serovar Typhimurium ST313 isolate B3589 from India

(2019) Jobin John Jacob et al.   INFECTION GENETICS AND EVOLUTION

The global burden of non-typhoidal salmonella invasive disease: a systematic analysis for the Global Burden of Disease Study 2017

(2019) Jeffrey D. Stanaway et al.   LANCET INFECTIOUS DISEASES

A Systematic Review and Meta-analysis of the Prevalence of Community-Onset Bloodstream Infections among Hospitalized Patients in Africa and Asia

(2019) Christian S. Marchello et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation

(2019) Sandra Van Puyvelde et al.   Nature Communications

Supporting evidence for a human reservoir of invasive non-Typhoidal Salmonella from household samples in Burkina Faso

(2019) Annelies S. Post et al.   PLoS Neglected Tropical Diseases

Early transmissible ampicillin resistance in zoonotic Salmonella enterica serotype Typhimurium in the late 1950s: a retrospective, whole-genome sequencing study

(2018) Alicia Tran-Dien et al.   LANCET INFECTIOUS DISEASES

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica

(2018) Nicole E. Wheeler et al.   PLoS Genetics

A genomic overview of the population structure of Salmonella

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

Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets

(2018) Anna Aulicino et al.   Nature Communications

Multilocus sequence typing of Salmonella Typhimurium reveals the presence of the highly invasive ST313 in Brazil

(2017) Fernanda Almeida et al.   INFECTION GENETICS AND EVOLUTION

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

(2017) Ea Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

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

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Larissa A. Singletary et al.   mBio

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

Mechanisms of drug resistance: quinolone resistance

(2015) David C. Hooper et al.   Annals of the New York Academy of Sciences

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

The Periplasmic Nitrate Reductase NapABC Supports Luminal Growth of Salmonella enterica Serovar Typhimurium during Colitis

(2015) Christopher A. Lopez et al.   INFECTION AND IMMUNITY

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

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

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

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories

(2013) E. Matuschek et al.   CLINICAL MICROBIOLOGY AND INFECTION

Virulence and stress-related periplasmic protein (VisP) in bacterial/host associations

(2013) Cristiano G. Moreira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ABC-Type Efflux Pump MacAB Protects Salmonella enterica serovar Typhimurium from Oxidative Stress

(2013) L. M. Bogomolnaya et al.   mBio

Characterization of the ELPhiS Prophage from Salmonella enterica Serovar Enteritidis Strain LK5

(2012) L. Farris Hanna et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

Identification of acquired antimicrobial resistance genes

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

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2012) Nicholas A Feasey et al.   LANCET

Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli LsoA and RnlA toxins

(2012) Yuichi Otsuka et al.   MOLECULAR MICROBIOLOGY

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

(2012) Chinyere K Okoro et al.   NATURE GENETICS

Genotypic Homogeneity of Multidrug Resistant S. Typhimurium Infecting Distinct Adult and Childhood Susceptibility Groups in Blantyre, Malawi

(2012) Chisomo L. Msefula et al.   PLoS One

Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance

(2011) A.-P. Magiorakos et al.   CLINICAL MICROBIOLOGY AND INFECTION

How To Become a Top Model: Impact of Animal Experimentation on Human Salmonella Disease Research

(2011) Renée M. Tsolis et al.   INFECTION AND IMMUNITY

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

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 the Salmonella enterica damX Gene Product, an Inner Membrane Protein Involved in Bile Resistance

(2009) J. Lopez-Garrido et al.   JOURNAL OF BACTERIOLOGY