Shigella + EIEC

Shigella and enteroinvasive E. coli (EIEC) data in AMRnet are drawn from Enterobase, which calls AMR genotypes using NCBI’s AMRFinderPlus and assigns lineages using cgMLST and hierarchical clustering. Last update: 5 August 2025.

Warning

The Shigella + EIEC 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: The logic used by Enterobase to classify genomes as Shigella or EIEC are detailed here. Shigella sonnei are monophyletic and labelled as lineage ‘S. sonnei’. For other Shigella, lineages are labeled by the species followed by the HC400 (HierCC) cluster ID (as this nomenclature has been shown to mirror the paraphyletic lineage structure of Shigella). EIEC lineages are labeled by ST (e.g. ‘EIEC ST99’).

• 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.