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Full information on isolate FRC1626 (id:3996)

Projects

This isolate is a member of the following projects:

2022_EuropeanWideReemergence_collection: Collection of the Hoefer et al. study on a large-scale Corynebacterium diphtheriae outbreak among migrant populations in Europe in 2022
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: 3996
isolate: FRC1626
species: C. diphtheriae
biovar: Mitis
tox gene PCR: Positive
tox production Elek: Positive
isolation year: 2022
country: France
continent: Europe
state or locality: Mainland France
travel history: TH
host: Human
source: SKINSWAB
infection or disease: CUTA
sender: Virginie Passet, Institut Pasteur, France
curator: Auto Tagger
update history: 6 updates show details
date entered: 2023-03-15
datestamp: 2025-07-18

Sequence bin

method: Unknown
contigs: 46
total length: 2,455,804 bp
max length: 362,452 bp
mean length: 53,388 bp
N50: 95,592
L50: 8
N90: 44,008
L90: 22
N95: 21,215
L95: 26
%GC: 53.57
Ns: 0
gaps: 0
loci tagged: 1,356

Show sequence bin

Assembly checks

Check	Status	Warn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Analysis

rMLST species identification

Rank	Taxon	Taxonomy	Support	Matches
SPECIES	Corynebacterium diphtheriae	Actinomycetota > Actinomycetes > Mycobacteriales > Corynebacteriaceae > Corynebacterium > Corynebacterium diphtheriae	100%

Analysis performed: 2024-12-12

Similar isolates (determined by LIN codes)

Scheme: cgMLST
LIN code: 0_0_126_2_0_0_0_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL302
Clonal group: ClG302
Genetic cluster: GC112

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Prefix	Threshold	Matching isolates
0_0_126_2_0_0	8	2
0_0_126_2_0_0_0	4	2
0_0_126_2_0_0_0_0	2	2
0_0_126_2_0_0_0_0_0	1	2
0_0_126_2_0_0_0_0_0_0	0	2
0	1220	2380
0_0	1035	2162
0_0_126	500	8
0_0_126_2	55	2
0_0_126_2_0	25	2
0_0_126_2_0_0	8	2
0_0_126_2_0_0_0	4	2
0_0_126_2_0_0_0_0	2	2
0_0_126_2_0_0_0_0_0	1	2
0_0_126_2_0_0_0_0_0_0	0	2

Similar isolates (determined by classification schemes)

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

Classification scheme	Underlying scheme	Clustering method	Mismatch threshold	Status	Group	Fields
Sublineage	cgMLST	Single-linkage	500	experimental	94 (7 isolates)	SL: 464
Genomic_cluster	cgMLST	Single-linkage	25	experimental	792 (2 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	94 (7 isolates)	SL: 464
Genomic_cluster	cgMLST	Single-linkage	25	experimental	792 (2 isolates)

Schemes and loci

All loci
- Classical schemes
- Other schemes
  - PBP
  - spuA_island
  - tox

Navigate and select schemes within tree to display allele designations

Tools

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