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Full information on isolate OXC6394 (id:16191)

Projects

This isolate is a member of the following projects:

Oxfordshire Human Surveillance
Defra FSA

This isolate is part of the sentinel surveillance scheme for human Campylobacteriosis in Oxfordshire which is a collaborative project between The Wellcome Trust Sanger Institute and The University of Oxford, funded by The Department for Environment, Food and Rural Affairs and The Food Standards Agency.

Use of Oxfordshire sentinel surveillance data must be cited in any publication or presentation making use of it.

Oxfordshire Human Surveillance YR1
929 Yr1 WGS isolates with complete MLST profiles

Provenance/meta data

id
16191
isolate
OXC6394
aliases
ERR084010; M7041; SC_RUN_7065_7#48
country
UK
continent
Europe
region
Oxfordshire
year
2011
month
8
sex
male
disease
gastroenteritis
source
human stool
epidemiology
sporadic case
species
Campylobacter jejuni
ENA accession
ERR084010 www.ebi.ac.uk
sender
Alison Cody
curator
Alison Cody, Department of Zoology, Oxford University, UK (E-mail: Alison.Cody@zoo.ox.ac.uk)
update history
98 updates show details
date entered
2012-01-18
datestamp
2019-06-26

Phenotypic fields

tetracycline genotypes 2
tetO

Publications (6)

  • Brown HL, Reuter M, Hanman K, Betts RP, van Vliet AH (2015). Prevention of biofilm formation and removal of existing biofilms by extracellular DNases of Campylobacter jejuni. PLoS One 10:e0121680
  • Cody AJ, Bray JE, Jolley KA, McCarthy ND, Maiden MCJ (2017). Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates. J Clin Microbiol 55:2086-2097
  • Cody AJ, McCarthy ND, Bray JE, Wimalarathna HM, Colles FM, Jansen van Rensburg MJ, Dingle KE, Waldenström J, Maiden MC (2015). Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom. Environ Microbiol Rep 7:782-8
  • Cody AJ, McCarthy ND, Jansen van Rensburg M, Isinkaye T, Bentley SD, Parkhill J, Dingle KE, Bowler IC, Jolley KA, Maiden MC (2013). Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J Clin Microbiol 51:2526-34
  • Dearlove BL, Cody AJ, Pascoe B, Méric G, Wilson DJ, Sheppard SK (2016). Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections. ISME J 10:721-9
  • Pearson BM, Louwen R, van Baarlen P, van Vliet AH (2015). Differential Distribution of Type II CRISPR-Cas Systems in Agricultural and Nonagricultural Campylobacter coli and Campylobacter jejuni Isolates Correlates with Lack of Shared Environments. Genome Biol Evol 7:2663-79

Sequence bin

contigs
40
total length
1,700,037 bp
max length
313,114 bp
mean length
42,501 bp
N50 contig number
4
N50 length (L50)
153,904
N90 contig number
11
N90 length (L90)
77,974
N95 contig number
13
N95 length (L95)
42,488
loci tagged
1,640
detailed breakdown
Display

Similar isolates (determined by classification schemes)

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Cjc_cgc_200C. jejuni / C. coli cgMLST v1.0Single-linkage200experimentalgroup: 1662 (536 isolates)
Cjc_cgc_100C. jejuni / C. coli cgMLST v1.0Single-linkage100experimentalgroup: 2745 (501 isolates)
Cjc_cgc_50C. jejuni / C. coli cgMLST v1.0Single-linkage50experimentalgroup: 4108 (70 isolates)
Cjc_cgc_25C. jejuni / C. coli cgMLST v1.0Single-linkage25experimentalgroup: 6380 (2 isolates)

Schemes and loci

Tools

Analysis: