Full information on isolate FRC0036 (id:109)
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
- 109
- isolate
- FRC0036
- species
- C. diphtheriae
- biovar
- Mitis
- tox gene PCR
- Negative
- tox production Elek
- Negative
- isolation year
- 2009
- city
- Mamoudzou
- country
- Mayotte
- continent
- Africa
- state or locality
- Mayotte
- travel history
- None
- host
- Human
- source
- Not documented
- infection or disease
- Wound
- accession number
- ERS1867709
- epidemic cluster
- Mayotte set 1
- sender
- Marina Barros, Institut Pasteur
- curator
- Mélanie Hennart, Institut Pasteur (E-mail: melanie.hennart@pasteur.fr)
- update history
- 1350 updates show details
- date entered
- 2017-02-13
- datestamp
- 2023-01-24
- outbreak or sporadic
- Sporadic
Publications (3)
- Dazas M, Badell E, Carmi-Leroy A, Criscuolo A, Brisse S (2018). Taxonomic status of Corynebacterium diphtheriae biovar Belfanti and proposal of Corynebacterium belfantii sp. nov. Int J Syst Evol Microbiol 68:3826-3831
- 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
- 34
- total length
- 2,413,085 bp
- max length
- 301,783 bp
- mean length
- 70,974 bp
- N50
- 202,424
- L50
- 5
- N90
- 34,281
- L90
- 15
- N95
- 21,918
- L95
- 19
- %GC
- 53.59
- 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 | 59 (7 isolates) | SL: 97 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 78 (3 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 59 (7 isolates) | SL: 97 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 78 (3 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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