E. coli Library for Integrated Pathogen Surveillance and Epidemiology
Typing, lineage annotations, and epidemiological metadata for every public E. coli genome — MLST, phylogroups, serotypes, CHTyper, plus country, source, host, and collection year. Filter. Verify. Download your accession list.
Nine interactive views. Every page supports live search, multi-column filtering, row selection, and one-click accession export.
Every genome linked to its country of origin, isolation source, host species, and collection year — extracted from NCBI BioSample. Filter by geography, drop the accessions into your pipeline, and answer questions like "all ST131 from urinary sources in West Africa" without writing a single line of code.
Four steps from query to genome download — no installation, no account, no limits.
Pick a typing scheme (MLST, Phylogroups, Serotypes, CHTyper) or the Master Table for everything at once.
Combine genotype + geography: e.g. ST131 +
B2 + United Kingdom + blood +
2010–2020.
Click 🧬 Accessions to download a plain-text list of matching genome accession IDs — one per line.
Feed the list to NCBI:
datasets download genome accession --inputfile list.txt
— that's it.
Antimicrobial Resistance Genomic Unified Surveillance · one family, seven ESKAPE pathogens
If you use ECLIPSE in your research, please cite the pipeline that produced its typing annotations:
EcoliTyper: Beckley B, Amarh V. EcoliTyper: a species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. BMC Bioinformatics. 2026. doi:10.1186/s12859-026-06529-6
Metadata: BioSample records from the NCBI Assembly database — country, isolation source, host, and collection date attributes.
Please also cite the specific downstream tools you used (mlst, ClermonTyping, SerotypeFinder, CHTyper, ABRicate, etc.) — see the EcoliTyper repository for the full list.