ReviewThe Journal of infectious diseases2021
Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework.
Review in The Journal of infectious diseases, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis 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
46 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Genomic Detection of Multidrug-Resistant H58 ST1 Salmonella Typhi in a South African Urban Waterway Reveals Epidemiological Links With Clinical Isolates.MicrobiologyOpen · 2026Article
- Azithromycin-resistantJAC-antimicrobial resistance · 2026Article
- Presence of globally prominent multidrug-resistant genotypes ofMicrobial genomics · 2026Article
- The typhoid Mary legacy: Genomic epidemiology uncovers contemporary carriage dynamics across two decades of enteric fever surveillance in England and Wales.PLoS neglected tropical diseases · 2026Article
- Evaluation of a machine learning system for genomic antimicrobial susceptibility determination on a clinically representative test set.Microbiology spectrum · 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
- A case of laboratory-acquired Salmonella Typhi infection due to phage typing in Japan: whole-genome sequencing confirms the source of infection.Access microbiology · 2026Article
- Article
- Comparative genomics ofVirulence · 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
- AmpliconTyper - a tool for analysing ONT multiplex PCR data from environmental and other complex samples.Microbial genomics · 2025Article
- Determining genotype and antimicrobial resistance of Salmonella Typhi in environmental samples by amplicon sequencing.PLoS neglected tropical diseases · 2025Article
- The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health.Genome medicine · 2025Article
- Antimicrobial susceptibility trends of S. Typhi and S. Paratyphi in a post-COVID-19 pandemic India, from a multicenter surveillance network.Scientific reports · 2025Article
- Emergence of carbapenem-resistantFrontiers in microbiology · 2025Article
- Monitoring antimicrobial resistance trends from global genomics data: amr.watch.PLOS global public health · 2025Article
- Azithromycin-resistant mph(A)-positive Salmonella enterica serovar Typhi in the United States.Journal of global antimicrobial resistance · 2024Article
- Conference report of the 2024 Antimicrobial Resistance Meeting.npj antimicrobials and resistance · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
In 2016, a whole-genome sequence (WGS)-based genotyping framework (GenoTyphi) was developed and provided a phylogenetically informative nomenclature for lineages of Salmonella Typhi, the etiological agent of typhoid fever. Subsequent surveillance studies have revealed additional epidemiologically important subpopulations, which require the definition of new genotypes and extension of associated software to facilitate the detection of antimicrobial resistance (AMR) mutations. Analysis of 4632 WGS provide an updated overview of the global S Typhi population structure and genotyping framework, revealing the widespread nature of haplotype 58 ([H58] 4.3.1) genotypes and the diverse range of genotypes carrying AMR mutations.
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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.