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Full information on isolate OXC8396 (id:28589)

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 YR3_dedup
DEFRA/FSA Oxfordshire Human Surveillance Year 3 isolates_de-duplicated

Provenance/meta data

id
28589
isolate
OXC8396
aliases
ERR484009; G73764; SC_RUN_12082_6#34
country
UK
continent
Europe
region
Oxfordshire
year
2013
month
10
sex
female
disease
gastroenteritis
source
human stool
epidemiology
sporadic case
species
Campylobacter jejuni
ENA accession
ERR484009 www.ebi.ac.uk
sender
Alison Cody, Department of Zoology, Oxford University, UK
curator
Sophie Hedges, Oxford University (E-mail: sophie.hedges@zoo.ox.ac.uk)
update history
71 updates show details
date entered
2014-03-14
datestamp
2019-06-18

Publications (3)

  • 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
  • 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
38
total length
1,634,543 bp
max length
485,721 bp
mean length
43,015 bp
N50 contig number
3
N50 length (L50)
180,732
N90 contig number
8
N90 length (L90)
80,693
N95 contig number
9
N95 length (L95)
42,573
loci tagged
1,664
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: 1663 (546 isolates)
Cjc_cgc_100C. jejuni / C. coli cgMLST v1.0Single-linkage100experimentalgroup: 3054 (42 isolates)
Cjc_cgc_50C. jejuni / C. coli cgMLST v1.0Single-linkage50experimentalgroup: 4516 (42 isolates)
Cjc_cgc_25C. jejuni / C. coli cgMLST v1.0Single-linkage25experimentalgroup: 6481 (42 isolates)
Cjc_cgc_10C. jejuni / C. coli cgMLST v1.0Single-linkage10experimentalgroup: 9814 (33 isolates)
Cjc_cgc_5C. jejuni / C. coli cgMLST v1.0Single-linkage5experimentalgroup: 13605 (10 isolates)

Schemes and loci

Tools

Analysis: