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Campylobacter MLST News and Updates

The core genome MLST (cgMLST) scheme (v1.0) for Campylobacter jejuni/coli is now available for use within the Campylobacter jejuni/coli databases.
The databases are now being powered by new genomics software. This allows much greater flexibility in locus handling and has the ability to handle whole genome data.
The isolate database has been normalized so that PubMed id values are now stored within their own table, rather than within fields in the isolate table. This means that now any number of papers can be associated with each isolate. The submission system now allows you to select a paper and submit a list of isolate id numbers that should be associated with it.
Submissions to the Campylobacter database should now be sent using the automated submissions system. This enables us to use a team of curators.
A list of recent publications that use or mention MLST in Campylobacter research is now generated automatically every day, providing an overview of the latest research utilising this technique.
Website layout integrated into the pubmlst.org style.
Advanced breakdown of isolate datasets is now available following a query. One field can be broken down by another, e.g. clonal complexes by year. You can also determine the frequencies of unique combinations of fields.
The Campylobacter MLST databases are now mirrored at http://ukmirror1.pubmlst.org/campylobacter/.
When displaying full information about an isolate following a search, if available the full citation is now displayed rather than just a PubMed id.
There is a new script available on the PubMLST (isolate) database that enables a user to query the database by cited publication.
There is a new script available on the PubMLST (isolate) database that enables a user to export full isolate information from a search as a tab-delimited text file.  These can be easily imported into spreadsheets or other analysis packages.  A new button will appear at the bottom of the isolate table when displaying data using the 'Browse database' page.
There is a new script available on the PubMLST (isolate) database that  provides a detailed breakdown of a displayed dataset.  A new link will appear at the bottom of the isolate table when displaying data using the 'Browse database' page.
A new server has been set up where the database has been split so that the allelic profiles and isolate data are stored separately.  This enables multiple isolate databases to be set up, all of which can connect to the profiles database (either locally or via the Internet) to query allelic profiles and allele sequences.  These isolate databases may be public or private and can represent true populations of bacteria, unlike the previous database that held data on whichever isolates were submitted.  The previous database has become the PubMLST isolate database.  Please contact the webmaster if you want further details about setting up your own isolate database that can connect to the profiles database via the Internet.

Citing the database

The preferred format for citing this website in publications is:

This publication made use of the Campylobacter Multi Locus Sequence Typing website (https://pubmlst.org/ campylobacter/) sited at the University of Oxford (Jolley & Maiden 2010, BMC Bioinformatics, 11:595). The development of this site has been funded by the Wellcome Trust.



Sequence database
Sequences: 851,917
MLST: 9,165
C. jejuni / C. coli cgMLST v1.0: 17,268

Isolate database
Isolates: 61,089
Last updated: 2018-03-16


Sequence database
Sequences: 2,989
C. concisus/curvus MLST: 130
C. fetus MLST: 69
C. helveticus MLST: 9
C. hyointestinalis MLST: 132
C. insulaenigrae MLST: 43
C. lanienae MLST: 171
C. lari MLST: 155
C. sputorum MLST: 16
C. upsaliensis MLST: 204

Isolate database
Isolates: 582
Last updated: 2018-02-06