Full information on isolate FRC0050 (id:114)
Projects
This isolate is a member of the following project:
- cgMLST set-up study
- Isolates included in the cgMLST study (publicly-available genomes and some isolates from the French NRC)
Provenance/primary metadata
- id
- 114
- isolate
- FRC0050
- species
- C. diphtheriae
- biovar
- Mitis
- tox gene PCR
- Positive
- tox production Elek
- Positive
- isolation year
- 2009
- city
- Mamoudzou
- country
- Mayotte
- continent
- Africa
- state or locality
- Mayotte
- travel history
- None
- host
- Human
- source
- Not documented
- infection or disease
- Respiratory
- accession number
- ERS4330850
- epidemic cluster
- Mayotte set 2
- sender
- Marina Barros, Institut Pasteur
- curator
- Virginie Passet, Institut Pasteur (E-mail: virginie.passet@pasteur.fr)
- update history
- 1345 updates show details
- date entered
- 2017-02-13
- datestamp
- 2022-07-01
- outbreak or sporadic
- Cluster
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
- Hennart M, Panunzi LG, Rodrigues C, Gaday Q, Baines SL, Barros-Pinkelnig M, Carmi-Leroy A, Dazas M, Wehenkel AM, Didelot X, Toubiana J, Badell E, Brisse S (2020). Population genomics and antimicrobial resistance in Corynebacterium diphtheriae. Genome Med 12:107
Sequence bin
- contigs
- 41
- total length
- 2,424,319 bp
- max length
- 537,084 bp
- mean length
- 59,130 bp
- N50
- 163,318
- L50
- 5
- N90
- 32,333
- L90
- 18
- N95
- 25,857
- L95
- 22
- %GC
- 53.49
- Ns
- 10
- gaps
- 1
- loci tagged
- 1,412
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
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 | 65 (5 isolates) | SL: 184 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 86 (2 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 65 (5 isolates) | SL: 184 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 86 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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