TyphiNET

Total Genomes

0

Total Genotypes

0

Global Overview of Salmonella Typhi
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Resistance frequencies within genotypes

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0255075100Percentage within genotype

Drug resistance trends

Data are plotted for years with N ≥ 10 genomes
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Resistance determinants within genotypes

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0255075100Percentage per genotype

Genotype distribution

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About TyphiNET
The TyphiNET dashboard collates antimicrobial resistance (AMR) and genotype (lineage) information extracted from whole genome sequence (WGS) data from the bacterial pathogen Salmonella Typhi, the agent of typhoid fever.
AMR determinants identified in the genome assemblies using Pathogenwatch are used to define drug resistance variables as follows. Multidrug resistant (MDR): resistance determinants for chloramphenicol (catA1 or cmlA), ampicillin (bla genes), and trimethoprim-sulfamethoxazole (at least one dfrA gene and at least one sul gene). Ciprofloxacin non-susceptible (CipNS): one or more of the quinolone resistance determining region (QRDR) mutations at gyrA-83, gyrA-87, parC-80, parC-84, gyrB-464 or presence of a plasmid-mediated quinolone resistance (PMQR) gene (qnrB, qnrD, qnrS). Ciprofloxacin resistant (CipR): QRDR triple mutant (gyrA-83 and gyrA-87, together with either parC-80 or parC-84), or (PMQR gene) together with gyrA-83, gyrA-87 and/or gyrB-464. Ceftriaxone resistant: presence of an extended - spectrum beta-lactamase (ESBL) gene. Extensively drug resistant (XDR): MDR plus CipR plus ESBL. Azithromycin resistant: mutation at acrB-717. See Argimon et al, 2021 and Carey et al, 2023 for details.
Genotypes are defined in the GenoTyphi scheme, details in Dyson & Holt, 2021 and Carey et al, 2023.
Data: Typhi genome and source data are curated by the Global Typhoid Genomics Consortium using Typhi Pathogenwatch, as described in Carey et al, 2023. Data displayed in the TyphiNET dashboard are filtered to include only genomes from unbiased sampling frames (e.g. routine or project-based enteric fever surveillance, as opposed to AMR-focused sampling or outbreak investigations). The TyphiNET database (genome-level line list) can be downloaded using the 'Download database' button above. To contribute Typhi genome data, please get in touch with the Global Typhoid Genomics Consortium Global Typhoid Genomics Consortium.

Documentation: Full documentation for the dashboard is available here.

Team: The TyphiNET dashboard is coordinated by Dr Zoe Dyson, Dr Louise Cerdeira and Prof Kat Holt, with support from the Wellcome Trust (Open Research Fund 219692/Z/19/Z; AMRnet project 226432/Z/22/Z), the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681EU_FLAG the London School of Hygiene & Tropical Medicine and Monash University.

Data last pulled from Pathogen Watch on 24/01/2024.

TyphiNET