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Full information on isolate KL2173 (id:4171)

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: 4171
isolate: KL2173
species: C. diphtheriae
biovar: Gravis
tox gene PCR: Positive
tox production Elek: Positive
isolation year: 2022
country: Germany
continent: Europe
travel history: LAT
host: human
source: SKINSWAB
infection or disease: CUTA
resistance info: Penicillin:0,19 mg/l; Ery:S; Clinda:S; Cipro:I; Vanco:S
comments: ST-8
sender: Annika Sprenger, Bavarian Health and Food Safety Authority (LGL)
curator: Auto Tagger
update history: 7 updates show details
date entered: 2023-03-15
datestamp: 2025-07-17
outbreak or sporadic: sporadic

Sequence bin

method: Unknown
contigs: 32
total length: 2,437,534 bp
max length: 347,693 bp
mean length: 76,173 bp
N50: 164,003
L50: 5
N90: 47,346
L90: 16
N95: 31,613
L95: 19
%GC: 53.49
Ns: 0
gaps: 0
loci tagged: 1,363

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_0_0_0_0_2_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL8
Clonal group: ClG8
Genetic cluster: GC29

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Prefix	Threshold	Matching isolates
0_0_0_0_0_0	8	5
0_0_0_0_0_0_2	4	1
0_0_0_0_0_0_2_0	2	1
0_0_0_0_0_0_2_0_0	1	1
0_0_0_0_0_0_2_0_0_0	0	1
0	1220	2380
0_0	1035	2162
0_0_0	500	88
0_0_0_0	55	88
0_0_0_0_0	25	13
0_0_0_0_0_0	8	5
0_0_0_0_0_0_2	4	1
0_0_0_0_0_0_2_0	2	1
0_0_0_0_0_0_2_0_0	1	1
0_0_0_0_0_0_2_0_0_0	0	1

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	1 (88 isolates)	SL: 8
Genomic_cluster	cgMLST	Single-linkage	25	experimental	1 (13 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	1 (88 isolates)	SL: 8
Genomic_cluster	cgMLST	Single-linkage	25	experimental	1 (13 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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