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Informing shigellosis prevention and control through pathogen genomics

https://doi.org/10.1101/2021.06.09.447709

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Age-related efficacy of Shigella O-specific polysaccharide conjugates in 1–4-year-old Israeli children

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Serotype replacement in disease after pneumococcal vaccination

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

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Shigellosis

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Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri

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Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study

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Morbidity and mortality due to shigella and enterotoxigenic Escherichia coli diarrhoea: the Global Burden of Disease Study 1990–2016

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Africa's $100-million Pathogen Genomics Initiative

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

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Deletion of toxin–antitoxin systems in the evolution of Shigella sonnei as a host-adapted pathogen

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Global phylogeography and evolutionary history of Shigella dysenteriae type 1

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Progress and pitfalls in Shigella vaccine research

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Clinical trials of Shigella vaccines: two steps forward and one step back on a long, hard road

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Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei

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Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

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Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa

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Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

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Author Correction: Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

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Improved protein structure prediction using predicted interresidue orientations

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Guidelines for the treatment of dysentery (shigellosis): a systematic review of the evidence

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QMEANDisCo—distance constraints applied on model quality estimation

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The Sequence Alignment/Map format and SAMtools

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Qualimap: evaluating next-generation sequencing alignment data

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QUAST: quality assessment tool for genome assemblies

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Prokka: rapid prokaryotic genome annotation

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Trimmomatic: a flexible trimmer for Illumina sequence data

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Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)

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AliView: a fast and lightweight alignment viewer and editor for large datasets

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Roary: rapid large-scale prokaryote pan genome analysis

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

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UpSetR: an R package for the visualization of intersecting sets and their properties

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QMEANDisCo—distance constraints applied on model quality estimation

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Shigella Isolates From the Global Enteric Multicenter Study Inform Vaccine Development

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Genome diversity of Shigella boydii

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Effect of Prior Infection with Virulent Shigella flexneri 2a on the Resistance of Monkeys to Subsequent Infection with Shigella sonnei

inferredcites →https://doi.org/10.1093/jac/dkx170openalex-snapshot

Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Shigella sonnei isolated from cases of diarrhoeal disease in England and Wales, 2015

inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot

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

inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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

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

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Interactive Tree Of Life (iTOL) v4: recent updates and new developments

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Epidemiologic Patterns of Acute Diarrhea and Endemic Shigella Infections in Children in a Poor Periurban Setting in Santiago, Chile

inferredcites →https://doi.org/10.1093/sysbio/syy032openalex-snapshot

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

inferredcites →https://doi.org/10.1093/ve/vew007openalex-snapshot

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

inferredcites →https://doi.org/10.1099/mgen.0.000171openalex-snapshot

Out of Asia: the independent rise and global spread of fluoroquinolone-resistant Shigella

inferredcites →https://doi.org/10.1101/2020.07.22.200840openalex-snapshot

An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes

inferredcites →https://doi.org/10.1128/aac.00483-19openalex-snapshot

Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates

inferredcites →https://doi.org/10.1128/aem.00165-19openalex-snapshot

In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification

inferredcites →https://doi.org/10.1128/iai.06174-11openalex-snapshot

Broadly Protective Shigella Vaccine Based on Type III Secretion Apparatus Proteins

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Shigella flexneri invasion plasmid antigens B and C: epitope location and characterization with monoclonal antibodies

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Identification of Epitope and Surface-Exposed Domains of Shigella flexneri Invasion Plasmid Antigen D (IpaD)

inferredcites →https://doi.org/10.1128/jcm.00614-09openalex-snapshot

Emergence of a New Multidrug-Resistant Serotype X Variant in an Epidemic Clone of Shigella flexneri

inferredcites →https://doi.org/10.1128/jcm.03527-14openalex-snapshot

Defining the Phylogenomics of Shigella Species: a Pathway to Diagnostics

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Prospective study of the association between serum antibodies to lipopolysaccharide O antigen and the attack rate of shigellosis

inferredcites →https://doi.org/10.1136/bmjgh-2019-002244openalex-snapshot

Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

inferredcites →https://doi.org/10.1177/2051013613500428openalex-snapshot

An update on vaccines against Shigella

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bModelTest: Bayesian phylogenetic site model averaging and model comparison

inferredcites →https://doi.org/10.1186/s13073-014-0090-6openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

inferredcites →https://doi.org/10.1371/journal.pcbi.1005595openalex-snapshot

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

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

inferredcites →https://doi.org/10.1371/journal.pcbi.1008543openalex-snapshot

PremPS: Predicting the impact of missense mutations on protein stability

inferredcites →https://doi.org/10.1371/journal.pmed.0030353openalex-snapshot

A Multicentre Study of Shigella Diarrhoea in Six Asian Countries: Disease Burden, Clinical Manifestations, and Microbiology

inferredcites →https://doi.org/10.1371/journal.pmed.1002055openalex-snapshot

South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study

inferredcites →https://doi.org/10.1371/journal.pone.0022663openalex-snapshot

Outer Membrane Protein A (OmpA) of Shigella flexneri 2a, Induces Protective Immune Response in a Mouse Model

inferredcites →https://doi.org/10.1371/journal.pone.0046095openalex-snapshot

A Novel Plasmid-Encoded Serotype Conversion Mechanism through Addition of Phosphoethanolamine to the O-Antigen of Shigella flexneri

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Vaccine Escape Recombinants Emerge after Pneumococcal Vaccination in the United States

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World health organization releases global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics

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Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

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

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