Full information on isolate CS18 (id:1315)

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
1315
isolate
CS18
alias
2019026
species
C. diphtheriae
isolation year
2019
country
Spain
continent
Europe
travel history
None
host
Human
source
Pharyngeal swab
accession number
SAMEA7617335
sender
Julien Guglielmini, Institut Pasteur, France
curator
Auto Tagger
update history
1311 updates show details
date entered
2021-04-09
datestamp
2025-07-17

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
42
total length
2,374,323 bp
max length
422,984 bp
mean length
56,532 bp
N50
177,008
L50
4
N90
72,243
L90
13
N95
37,204
L95
15
%GC
53.45
Ns
0
gaps
0
loci tagged
1,309

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_19_4_1_13_0_0_0_0
Species
C. diphtheriae
Lineage
0_0
Sublineage
SL32
Clonal group
ClG32
Genetic cluster
GC28

Show all thresholds

PrefixThresholdMatching isolates
0_0_19_4_1_1381
0_0_19_4_1_13_041
0_0_19_4_1_13_0_021
0_0_19_4_1_13_0_0_011
0_0_19_4_1_13_0_0_0_001
012202380
0_010352162
0_0_19500102
0_0_19_45553
0_0_19_4_12545
0_0_19_4_1_1381
0_0_19_4_1_13_041
0_0_19_4_1_13_0_021
0_0_19_4_1_13_0_0_011
0_0_19_4_1_13_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-linkage500experimental23 (30 isolates)
SL: 32
Genomic_clustercgMLSTSingle-linkage25experimental23 (17 isolates)
SublineagecgMLSTSingle-linkage500experimental23 (30 isolates)
SL: 32
Genomic_clustercgMLSTSingle-linkage25experimental23 (17 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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