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C. jejuni/C. coli core genome MLST (cgMLST) scheme

A C. jejuni / C. coli core genome MLST (cgMLST) scheme v1.0 has been defined from 2,742 Oxfordshire Human Surveillance genomes, for use in the analysis of human disease isolates.

Loci appearing in 95% or more of genomes were detected, using the Genome Comparator function of BIGSdb, from the 1,643 loci defined by the re-annotation of the NCTC11168 genome (Gundogdu et al., 2007). Potential paralogues were identified in 5 subsets of 10 isolates by running Genome Comparator and excluding paralogous loci from distance matrix calculations; firstly, when loci were paralogous in all isolates (default BLAST settings) and secondly when loci were paralogous in any isolates (min 90% sequence similarity BLAST setting). Sequence similarities to loci thus detected were identified in further loci using GeneDB. This resulted in the identification of 22 potential paralogous loci which were removed from the original 95% core list to provide a cgMLST scheme of 1,343 loci.

This scheme is available for selection within the sequence definition and isolate databases. It can also be accessed via the RESTful API.

Citing the database

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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.

Status

jejuni/coli

Sequence database
Sequences: 833169
Profiles:
MLST: 9021
C. jejuni / C. coli cgMLST v1.0: 16695

Isolate database
Isolates: 54800
Last updated: 2017-10-19

Non-jejuni/coli

Sequence database
Sequences: 2951
Profiles:
C. concisus/curvus MLST: 130
C. fetus MLST: 69
C. helveticus MLST: 9
C. hyointestinalis MLST: 131
C. insulaenigrae MLST: 43
C. lanienae MLST: 171
C. lari MLST: 138
C. sputorum MLST: 16
C. upsaliensis MLST: 204

Isolate database
Isolates: 513
Last updated: 2017-09-15