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Submission of data

All users are welcome to submit their new allele sequences to our database for Clostridioides difficile.  This information will be made available on this web site.

In order to maintain the quality of the data, the databases are curated and all submissions will be checked before entry.

Automated submission system

We have introduced an automated system for submission of new alleles, profiles and isolate data.

Users will need an account in order to use the submission system. Please register if you do not already have an account.

Please read the submission system documentation for further details.

Template files

The template files listed below will help you upload your data in the correct format.

Database Template Version Field description
Allelic profiles database Download 2010-08-24
Isolates database Download 2010-08-24 Fields

(in some browsers you may have to right-click and select 'Save Target As' or 'Save Link As').

In the isolate submission template you can add alternative names for your isolate. These are entered in the 'aliases' field as a semi-colon separated list. You can also add publications that refer to an isolate by entering a semi-colon separated list of PubMed id numbers to the 'references' field. Use the field description link in the table above to assist you in filling out the template.

Citing the database

The preferred format for citing this website in publications is:

This publication made use of the Clostridium difficile Multi Locus Sequence Typing website (https://pubmlst.org/ cdifficile/) sited at the University of Oxford (Jolley et al. Wellcome Open Res 2018, 3:124 [version 1; referees: 2 approved]). The development of this site has been funded by the Wellcome Trust.


Sequence database
Sequences: 2,856
Profiles (MLST): 692
Last updated: 2020-09-17

Isolate database
Isolates: 1,780
Last updated: 2020-09-16