ArticleNature communications2021
Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed, 103 citations in OpenAlex.
- Draft genome sequences of 22Microbiology resource announcements · 2026Article
- Investigation of an outbreak ofMicrobial genomics · 2026Article
- Genome sequence ofMicrobiology resource announcements · 2026Article
- Comparative genomic, phenotypic, and clinical characterization of ST11-KL25 and ST11-KL64 hypervirulent carbapenem-resistantAntimicrobial agents and chemotherapy · 2026Article
- The natural history of the emergence of sexually transmissible shigellosis.Microbial genomics · 2026Review
- A public resource of 15 genomically characterized representative strains ofMicrobial genomics · 2026Article
- Beyond presence and frequency: a determinant-level framework for interpreting AMR dissemination in One Health surveillance.Frontiers in bioinformatics · 2026Article
- Article
- Article
- Emergence of a novel genotype of extensively drug-resistantAntimicrobial stewardship & healthcare epidemiology : ASHE · 2026Article
- Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference.PLoS pathogens · 2025Article
- Global epidemiological insights on the antimicrobial resistance ofMicrobial genomics · 2025Article
- Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi.Genome medicine · 2025Article
- Integrating serotyping, MLST, and phenotypic data: decoding the evolutionary drivers ofApplied and environmental microbiology · 2025Article
- Enhanced virulence and stress tolerance are signatures of epidemiologically successful Shigella sonnei.Nature communications · 2025Article
- The emergence of sexually transmissibleMicrobial genomics · 2025Article
- Epidemiologic and Genomic Investigation of Sexually Transmitted Shigella sonnei, England.Emerging infectious diseases · 2025Article
- Shigella sonnei: epidemiology, evolution, pathogenesis, resistance and host interactions.Nature reviews. Microbiology · 2025Review
- Genomic Modeling of an Outbreak of Multidrug-Resistant Shigella sonnei, California, USA, 2023-2024.Emerging infectious diseases · 2025Article
- Lessons from 5 Years of Routine Whole-Genome Sequencing for Epidemiologic Surveillance of Shiga Toxin-Producing Escherichia coli, France, 2018-2022.Emerging infectious diseases · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 10 institutions in 3 countries.
Funding
Abstract
Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.