Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

Human intestinal enteroids as a model system of Shigella pathogenesis

(2019) Benjamin J. Koestler et al.   INFECTION AND IMMUNITY

Virulence-related genes are associated with clinical and nutritional outcomes of Shigella/Enteroinvasive Escherichia coli pathotype infection in children from Brazilian semiarid region: A community case-control study

(2019) Mariana Bona et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

pyseer: a comprehensive tool for microbial pangenome-wide association studies

(2018) John A Lees et al.   BIOINFORMATICS

Molecular characterization of virulence and antimicrobial resistance profile of Shigella species isolated from children with moderate to severe diarrhea in northeastern Brazil

(2018) Pedro Henrique Quintela Soares Medeiros et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Phylogenetic comparison of enteroinvasive Escherichia coli isolated from cases of diarrhoeal disease in England, 2005–2016

(2018) Lauren A. Cowley et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species

(2018) Kate S. Baker et al.   Nature Communications

Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance

(2018) Kate S. Baker et al.   Scientific Reports

Comparative genomics of phenotypic antimicrobial resistances in methicillin-resistant Staphylococcus pseudintermedius of canine origin

(2018) Alice Wegener et al.   VETERINARY MICROBIOLOGY

A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events

(2018) Magali Jaillard et al.   PLoS Genetics

Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease

(2017) Rahajeng N. Tunjungputri et al.   mBio

Higher classification sensitivity of short metagenomic reads with CLARK- S

(2016) Rachid Ounit et al.   BIOINFORMATICS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

A screening algorithm for diagnosing bacterial gastroenteritis by real-time PCR in combination with guided culture

(2016) P. Van Lint et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

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

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

Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study

(2016) Jie Liu et al.   LANCET

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

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

(2016) John A. Lees et al.   Nature Communications

Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

(2016) Emily A. Pettengill et al.   Frontiers in Microbiology

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

The advent of genome-wide association studies for bacteria

(2015) Peter E Chen et al.   CURRENT OPINION IN MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

(2015) Katrine G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Escherichia colidiversity in the lower intestinal tract of humans

(2015) David M. Gordon et al.   Environmental Microbiology Reports

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

(2015) Thomas R Connor et al.   eLife

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Shigella Isolates From the Global Enteric Multicenter Study Inform Vaccine Development

(2014) S. Livio et al.   CLINICAL INFECTIOUS DISEASES

Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association

(2014) Md Tauqeer Alam et al.   Genome Biology and Evolution

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

(2013) S. K. Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

(2012) Kathryn E Holt et al.   NATURE GENETICS

Differentiation between Shigella, enteroinvasive Escherichia coli (EIEC) and noninvasive Escherichia coli

(2011) M. J. C. Beld et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Changing species distribution and antimicrobial susceptibility pattern of Shigella over a 29-year period (1980–2008)

(2010) F. KHATUN et al.   EPIDEMIOLOGY AND INFECTION

Evaluation of a Gastroenteritis Severity Score for Use in Outpatient Settings

(2010) S. B. Freedman et al.   PEDIATRICS