Escherichia coli

Escherichia coli data in AMRnet are drawn from Enterobase, which calls AMR genotypes using NCBI’s AMRFinderPlus and assigns lineages using MLST, cgMLST and hierarchical clustering. Last update: 5 August 2025.

Warning

The E. coli 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