Escherichia coli metadata files obtained from isolates listed in Enterobase and PATRIC databases.

SampleMiner (SM) is a Python script that helps researchers dependent on limited internet resources to locally perform microbial isolates sampling, metadata retrieval and whole-genome sequences (WGS) download, provided the metadata pages of the online database can be downloaded as comma-separated value (csv) files. The metadata tab-separated value (tsv) files listed in this Figshare item were used during the development of SM code. These files contain all E. coli isolates metadata obtained from Enterobase on 18/11/2021 and from PATRIC on 29/9/2021, using Escherichia or Shigella as combined keywords. The originally downloaded csv files were converted into the tsv files.