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Full information on isolate UK03 (id:4008)

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: 4008
isolate: UK03
species: C. diphtheriae
tox gene PCR: Positive
tox production Elek: Positive
isolation year: 2022
city: Newcastly-upon-Tyne
country: UK
continent: Europe
travel history: FR
host: Human
source: SKINSWAB
infection or disease: CUTA
sender: Josh D'Aeth, UKHSA, UK
curator: Auto Tagger
update history: 6 updates show details
date entered: 2023-03-15
datestamp: 2025-07-17

Sequence bin

method: Unknown
contigs: 41
total length: 2,473,478 bp
max length: 307,392 bp
mean length: 60,329 bp
N50: 119,206
L50: 7
N90: 39,096
L90: 19
N95: 24,849
L95: 23
%GC: 53.43
Ns: 0
gaps: 0
loci tagged: 1,366

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_18_0_0_7_0_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL384
Clonal group: ClG384
Genetic cluster: GC3

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Prefix	Threshold	Matching isolates
0_0_18_0_0_7	8	88
0_0_18_0_0_7_0	4	87
0_0_18_0_0_7_0_0	2	84
0_0_18_0_0_7_0_0_0	1	34
0_0_18_0_0_7_0_0_0_0	0	34
0	1220	2380
0_0	1035	2162
0_0_18	500	127
0_0_18_0	55	119
0_0_18_0_0	25	119
0_0_18_0_0_7	8	88
0_0_18_0_0_7_0	4	87
0_0_18_0_0_7_0_0	2	84
0_0_18_0_0_7_0_0_0	1	34
0_0_18_0_0_7_0_0_0_0	0	34

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	131 (119 isolates)	SL: 384
Genomic_cluster	cgMLST	Single-linkage	25	experimental	217 (115 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	131 (119 isolates)	SL: 384
Genomic_cluster	cgMLST	Single-linkage	25	experimental	217 (115 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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