How to Find ECRC Genomes in NCBI Pathogen Detection

Explore thousands of genome-sequenced E. coli strains submitted by the ECRC through NCBI Pathogen Detection tool. This guide provides clear instructions for locating and exploring these publicly available sequences.

1. Access the NCBI Pathogen Detection Platform

Visit NCBI Pathogen Detection.
Under the Data Resources section on the right-hand side, click on "Isolates Browser."

2. Open the Filter Menu

At the top of the Isolates Browser page, click the "Filters" button to access filtering options.

  • On the left, check the box for "Organism group."
    • Then, from the right-hand list, select "E. coli and Shigella."
  • Scroll further down the filter list and find "Collected by."
    • Click this option, then select "E. coli Reference Center."

You are now viewing E. coli isolates submitted by the ECRC.

3. Understand the Table Layout

Once you apply the filters to view ECRC-submitted E. coli strains, you’ll see a table with detailed information about each isolate. Here's a guide to what the columns mean:

  • # – A sequential row number in the current browser view (not related to strain identity).

  • Organism group – Displays the species or species group, such as E. coli and Shigella.

  • Strain –  ECRC ID in format XX.YYYY (XX = year, YYYY = strain number)

  • Isolate identifiers – Alternative names or aliases that may be linked to other public submissions.

  • Isolate – Clickable link to a phylogenetic tree that places the isolate in the context of genetically similar strains.

  • Create date –Date the record was added to NCBI (not isolation date).

  • Location / Isolation source – Where the strain was isolated (e.g., poultry, cattle, water) and geographic metadata if available.

  • SNP cluster – Genomic grouping based on similarity. Isolates are placed in a cluster if they are within 50 SNPs of another isolate. Clicking the cluster ID reveals a tree of related strains.

  • Isolation type – Clinical: human-associated, Environmental: non-human (e.g., animal, food, water)

  • Min-same / Min-diff – SNP distance to closest same-type and different-type isolate. 

  • Biosample – Link to the full metadata for the isolate in NCBI’s BioSample database.

  • Assembly – If a whole genome assembly is available, this column links directly to the sequence data.

4. Customize What You See

Click the “Choose columns” icon in the table header to personalize your view.

Recommended columns to add:

  • Stress genotypes – Genes linked to environmental stress survival

  • AMR genotypes – Genes related to antimicrobial resistance

  • Virulence genotypes – Genes associated with host interaction or disease

Drag fields you want into the visible table on the left; remove others by dragging them out.

5. Download the Data

To save and sort the table offline, click the "Download" button at the top of the Isolates Browser.
The data will be downloaded as a spreadsheet that can be opened in Excel or similar tools.

Questions or Need Help?

For assistance locating a specific isolate or understanding metadata fields, please contact:
Ed Dudley – ECRC@psu.edu