Salmonella (invasive non-typhoidal)

Salmonella (invasive non-typhoidal) 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 iNTS dashboard currently includes all genomes identified as serotype Typhimurium or Enteritidis (which account for >90% of iNTS), and identifies lineages thereof using MLST. Last update: 5 August 2025.

The invasive non-typhoidal Salmonella (iNTS) dashboard is populated with data from specific Salmonella enterica lineages that are associated with invasive disease in low-income countries; namely serotype Typhimurium (ST19, ST313 and sublineages thereof as defined by Van Puyvelde et al) and Enteritidis (Central/Eastern and West African clades as defined by Fong et al). Together these account for >90% of iNTS.

Warning

The iNTS 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 iTYM (invasive Typhimurium) or iENT (invasive Enteritidis) followed by the lineage name, defined from cgMLST as follows:

  • iTYM ST19-L1: HC150=305

  • iTYM ST19-L3: HC150=1547

  • iTYM ST19-L4: HC150=48

  • iTYM ST313-L1: HC150=9882

  • iTYM ST313-L2: HC150=728 and HC50=728

  • iENT CEAC: HC150=12675

  • iENT WAC: HC150=2452

• 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.