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I have a list of about 900 E.coli genome ids (Genbank plus NCTC ids), e.g.:

NCTC8196_1
NCTC11105_1
CP027464.1
CP027459.1
CP027363.1
CP027388.1
CP027355.1
CP027675.1
CP027445.1
CP027325.1
CP027219.1

and I would like to find pathogenicity metadata for them so that I can classify the molecular data I found with the metadata.

Is there a way to get a table of metadata from these genomes that I can use to associate with my molecular data?

NOTES:

After some searching online, I found Enterobase (http://enterobase.warwick.ac.uk), but it seems the site is mostly dedicated to MLST typing, thus they use different naming conventions than the Genbank id. Maybe there is a way to link the info in Enterobase with Genbank ids somehow?

It seems like Enterobase contains project ids, e.g. PRJNA218110. These project ids can also be found on the other side in the GenBank entries, for which we could associate the GenBank chromosomal ids.

Searching for PRJNA218110 in Enterobase gives a very long list of entries that seem to be from Illumina sequencing data, but in this list, the 'Path/Nonpath' column is always empty.

Enterobase seems to contain lots of entries with useful information, such as: the strain is pathogenic, and produced diarrhea in humans. So a table with entries like the one below would be very useful:

Genbank_id: CPXXXXXXX.1
Path/Nonpath: Pathogenic
Disease: Diarrhea

Genbank_id: CPYYYYYYY.1
Path/Nonpath: Nonpathogenic
Disease: NA
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  • $\begingroup$ What kind of data, exactly? CP027459.1 is an entire genome. Are you trying to see if this strain is a pathogen? If so, for what species? Are you instead trying to see if mutations in this genome can be pathogenic for the bacterium? Please edit and clarify what you're after. $\endgroup$
    – terdon ♦
    Commented Oct 9, 2019 at 10:44
  • $\begingroup$ I added a comment now referring to what I can find in Enterobase, thanks @terdon . $\endgroup$
    – 719016
    Commented Oct 9, 2019 at 10:51
  • $\begingroup$ Thanks! So you are looking for information on which of these bacteria are pathogens in humans? Humans only or do you also want pathogenicity information on any species? $\endgroup$
    – terdon ♦
    Commented Oct 9, 2019 at 11:00
  • $\begingroup$ Humans mainly, but any would be great $\endgroup$
    – 719016
    Commented Oct 9, 2019 at 11:56

1 Answer 1

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you can use BacDive. This is the largest database for bacterial metadata.: https://bacdive.dsmz.de/ e.g. you can search for the sequence accession "NCTC8196" and you would get the metadata of the according strain: https://bacdive.dsmz.de/search?search=NCTC8196

What kind of data is available, is highly dependent on the strain. Usually type strains are more rich on data that others.

For further questions don't hesitate to contact us: [email protected]

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