Salmonella (non-typhoidal)¶
Nontyphoidal Salmonella data in AMRnet are drawn from Enterobase, which calls AMR genotypes using NCBI’s AMRFinderPlus, assigns lineages using MLST, cgMLST and hierarchical clustering, and assigns serotypes using SISTR. The Salmonella (non-typhoidal) dashboard includes all genomes classified as S. enterica subsp. enterica (based on hierarchical clustering level 2850, HC2850=2), and excluding all genomes with predicted serotype Typhi or Paratyphi A/B/C. Last update: 5 August 2025.
For information about Salmonella Typhi, please see the Typhi dashboard. Inclusion of Paratyphi A is planned for 2026.
Warning
The non-typhoidal Salmonella data used in AMRnet are not yet curated for purpose-of-sampling, and therefore reflect the biases of global sequencing efforts which may be skewed towards sequencing AMR strains and/or outbreaks. Data curation efforts are ongoing however until then, please be careful when interpreting the data in the dashboard.
Variable definitions¶
Lineages - Lineages are labeled by 7-locus sequence type (ST).
AMR determinants: - Enterobase identifies AMR determinants using NCBI’s AMRFinderPlus run with default settings. AMRnet imports these AMR genotype calls, and assigns them to drugs/classes in the dashboard using the Subclass curated in refgenes, see the table.