Full information on isolate CS18 (id:1315)
Projects
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
Assembly checks
| Check | Status | Warn/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
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 | 23 (30 isolates) | SL: 32 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 23 (17 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 23 (30 isolates) | SL: 32 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 23 (17 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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