Full information on isolate CS6 (id:1326)

Projects

This isolate is a member of the following projects:

Hennart_diphtOscan_2023_OtherIsolates
Publicly-available genomes and isolates from the French NRC (2018-2021)
DelgadoBlas_LINcodes_2025
Dataset of 1,665 isolates of C. diphtheriae, C. belfantii and C. rouxii used for the population structure analysis of C. diphtheriae sensu lato.

Provenance/primary metadata

id
1326
isolate
CS6
alias
2017001
species
C. diphtheriae
isolation year
2017
country
Spain
continent
Europe
travel history
None
host
Human
source
Oropharyngeal swab
accession number
SAMEA7617324
sender
Julien Guglielmini, Institut Pasteur, France
curator
Auto Tagger
update history
1288 updates show details
date entered
2021-04-09
datestamp
2025-07-18

Publications (2)

  • Guglielmini J, Hennart M, Badell E, Toubiana J, Criscuolo A, Brisse S (2021). Genomic Epidemiology and Strain Taxonomy of Corynebacterium diphtheriae. J Clin Microbiol 59:e0158121
  • Hoefer A, Pampaka D, Herrera-León S, Peiró S, Varona S, López-Perea N, Masa-Calles J, Herrera-León L (2021). Molecular and Epidemiological Characterization of Toxigenic and Nontoxigenic Corynebacterium diphtheriae, Corynebacterium belfantii, Corynebacterium rouxii, and Corynebacterium ulcerans Isolates Identified in Spain from 2014 to 2019. J Clin Microbiol 59:

Sequence bin

method
Illumina
contigs
49
total length
2,442,235 bp
max length
345,312 bp
mean length
49,842 bp
N50
125,186
L50
6
N90
30,081
L90
18
N95
19,691
L95
23
%GC
53.64
Ns
0
gaps
0
loci tagged
1,298

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Similar isolates (determined by LIN codes)

Scheme
cgMLST
LIN code
0_0_197_9_1_1_0_0_0_0
Species
C. diphtheriae
Lineage
0_0
Sublineage
SL5
Clonal group
ClG5
Genetic cluster
GC23

Show all thresholds

PrefixThresholdMatching isolates
0_0_197_9_1_181
0_0_197_9_1_1_041
0_0_197_9_1_1_0_021
0_0_197_9_1_1_0_0_011
0_0_197_9_1_1_0_0_0_001
012202242
0_010352024
0_0_19750055
0_0_197_95534
0_0_197_9_12519
0_0_197_9_1_181
0_0_197_9_1_1_041
0_0_197_9_1_1_0_021
0_0_197_9_1_1_0_0_011
0_0_197_9_1_1_0_0_0_001

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 thresholdStatusGroupFields
SublineagecgMLSTSingle-linkage500experimental24 (53 isolates)
SL: 5
Genomic_clustercgMLSTSingle-linkage25experimental150 (17 isolates)
SublineagecgMLSTSingle-linkage500experimental24 (53 isolates)
SL: 5
Genomic_clustercgMLSTSingle-linkage25experimental150 (17 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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