Full information on isolate CD201 (id:3852)
Projects
This isolate is a member of the following project:
- 2022_EuropeanWideReemergence_collection
- Collection of the Hoefer et al. study on a large-scale Corynebacterium diphtheriae outbreak among migrant populations in Europe in 2022
Provenance/primary metadata
- id
- 3852
- isolate
- CD201
- species
- C. diphtheriae
- biovar
- Mitis
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2022
- city
- Bolzano
- country
- Italy
- continent
- Europe
- state or locality
- Trentino-Alto Adige
- travel history
- Iraq-Balkan route-north Italy
- host
- human
- source
- skin
- infection or disease
- Cutaneous
- sender
- Monica Monaco, Istituto Superiore di Sanità -Rome-Italy
- curator
- Federica Palma, Institut Pasteur, Paris, France (E-mail: federica.palma@pasteur.fr)
- update history
- 4 updates show details
- embargo history
- show details
- date entered
- 2023-01-31
- datestamp
- 2023-02-07
Sequence bin
- method
- Ion Torrent
- contigs
- 76
- total length
- 2,442,069 bp
- max length
- 336,734 bp
- mean length
- 32,133 bp
- N50
- 114,066
- L50
- 7
- N90
- 25,572
- L90
- 22
- N95
- 16,716
- L95
- 28
- %GC
- 53.55
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,344
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_21_0_4_0_0_0_1_0
- Species
- C. diphtheriae
- Lineage
- 0_0
- Sublineage
- SL377
- Clonal group
- ClG377
- Genetic cluster
- GC2
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_21_0_4_0 | 8 | 155 |
| 0_0_21_0_4_0_0 | 4 | 154 |
| 0_0_21_0_4_0_0_0 | 2 | 148 |
| 0_0_21_0_4_0_0_0_1 | 1 | 114 |
| 0_0_21_0_4_0_0_0_1_0 | 0 | 111 |
| 0 | 1220 | 2380 |
| 0_0 | 1035 | 2162 |
| 0_0_21 | 500 | 200 |
| 0_0_21_0 | 55 | 183 |
| 0_0_21_0_4 | 25 | 155 |
| 0_0_21_0_4_0 | 8 | 155 |
| 0_0_21_0_4_0_0 | 4 | 154 |
| 0_0_21_0_4_0_0_0 | 2 | 148 |
| 0_0_21_0_4_0_0_0_1 | 1 | 114 |
| 0_0_21_0_4_0_0_0_1_0 | 0 | 111 |
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 | 38 (183 isolates) | SL: 377 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 817 (142 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 38 (183 isolates) | SL: 377 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 817 (142 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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