Full information on isolate ERR2173855 (id:707)
Projects (4)
This isolate is a member of the following projects:
yemen2019 public
Yemen 2017-2020 outbreak
50 isolates
cgMLST set-up study public
Isolates included in the cgMLST study (Guglielmini et al. J CLin Microbiol 2021 https://pubmed.ncbi.nlm.nih.gov/34524891/)
440 isolates
Hennart_diphtOscan_2023_OtherIsolates public
Publicly-available genomes and isolates from the French NRC (2018-2021)
1,250 isolates
Provenance/primary metadata
- id
- 707
- isolate
- ERR2173855
- alias
- Cd_11
- species
- C. diphtheriae
- isolation year
- 2015
- city
- Somalia
- country
- Somalia
- continent
- Africa
- travel history
- Not documented
- host
- Human
- infection or disease
- wound
- accession number
- PRJEB14914
- epidemic cluster
- Germany-Switzerland set 1
- sender
- Melody Dazas, Institut Pasteur
- curator
- Auto Tagger
- update history
- 20 updates show details
- date entered
- 2018-05-29
- datestamp
- 2025-07-18
- 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
- Meinel DM, Kuehl R, Zbinden R, Boskova V, Garzoni C, Fadini D, Dolina M, Blümel B, Weibel T, Tschudin-Sutter S, Widmer AF, Bielicki JA, Dierig A, Heininger U, Konrad R, Berger A, Hinic V, Goldenberger D, Blaich A, Stadler T, Battegay M, Sing A, Egli A (2016). Outbreak investigation for toxigenic Corynebacterium diphtheriae wound infections in refugees from Northeast Africa and Syria in Switzerland and Germany by whole genome sequencing. Clin Microbiol Infect 22:1003.e1-1003.e8
Sequence bin
- method
- Unknown
- contigs
- 47
- total length
- 2,457,313 bp
- max length
- 315,865 bp
- mean length
- 52,284 bp
- N50
- 133,271
- L50
- 6
- N90
- 41,410
- L90
- 17
- N95
- 30,282
- L95
- 20
- %GC
- 53.55
- Ns
- 99
- gaps
- 1
- loci tagged
- 1,373
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Minimum N50 |
Similar isolates (determined by LIN codes)
- Scheme
- cgMLST
- LIN code
- 0_0_164_2_0_0_0_2_0_0
- Species
- C. diphtheriae
- Lineage
- 0_0
- Sublineage
- SL447
- Clonal group
- ClG473
- Genetic cluster
- GC155
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 | 13 (8 isolates) | SL: 473 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 13 (3 isolates) | |
| Sublineage | cgMLST | Single-linkage | 500 | experimental | 13 (8 isolates) | SL: 473 |
| Genomic_cluster | cgMLST | Single-linkage | 25 | experimental | 13 (3 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Analysis:
Export: