ArticleNature communications2016
An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers, 2 of them syntheses that pooled it.
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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.
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Who cites it
125 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
- A Systematic Review on Antimicrobial Resistance amongThe American journal of tropical medicine and hygiene · 2020Pooled it
- Homologous and heterologous re-challenge with Salmonella Typhi and Salmonella Paratyphi A in a randomised controlled human infection model.PLoS neglected tropical diseases · 2020Trial
- Treatment responses to Azithromycin and Ciprofloxacin in uncomplicated Salmonella Typhi infection: A comparison of Clinical and Microbiological Data from a Controlled Human Infection Model.PLoS neglected tropical diseases · 2019Trial
- Global transmission dynamics of antibiotic resistance genes: Foodborne pathways as the critical link to humans.One health (Amsterdam, Netherlands) · 2026Article
- Emergence of Genotype 2.3.1 Multidrug-Resistant Salmonella enterica Serovar Typhi Strain, West Africa, 2021-2025.Emerging infectious diseases · 2026Article
- Azithromycin-resistantJAC-antimicrobial resistance · 2026Article
- Presence of globally prominent multidrug-resistant genotypes ofMicrobial genomics · 2026Article
- Global genomic surveillance uncovers emergence and spatiotemporal patterns of World Health Organization priority antibiotic resistance in invasive Salmonella.Nature communications · 2026Article
- Cumulative cgMLST provides increased discrimination of nested phylogenetic groups.Genome medicine · 2026Article
- Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology.Nature communications · 2026Article
- Article
- Performance of mechanically sheared DNA in multiplexed Oxford Nanopore sequencing forMicrobial genomics · 2026Article
- Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens.PLoS biology · 2026Article
- Whole-Genome Sequencing for Antimicrobial Resistance Detection: A Simulation-Based Evaluation of WHO-Recommended Workflow in Pakistan.Pakistan journal of medical sciences · 2026Article
- AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance.Nucleic acids research · 2026Article
- Genomic characterization of Salmonella enterica isolates causing typhoid among Ghanaian patients.PloS one · 2026Article
- Integrative genomic and molecular dynamics characterisation ofFrontiers in microbiology · 2026Article
- Carbapenem-Resistant Salmonella Typhi Infection in Traveler Returning to Germany from India, 2024.Emerging infectious diseases · 2025Article
- Emergence of azithromycin and ciprofloxacin non-susceptible genotype 4.2.2Antimicrobial agents and chemotherapy · 2025Article
65 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.
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