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Full information on isolate CD1008 (id:2336)

Projects

This isolate is a member of the following projects:

SL453 study in 2022: See Arcari et al. Microbial Genomics 2023 (IDs 2315 and 2336 were added after publication)
Hennart_diphtOscan_2023_OtherIsolates: Publicly-available genomes and isolates from the French NRC (2018-2021)
DelgadoBlas_LINcodes_2025: Dataset of 1,665 isolates of C. diphtheriae, C. belfantii and C. rouxii used for the population structure analysis of C. diphtheriae sensu lato.

Provenance/primary metadata

id: 2336
isolate: CD1008
alias: PC0696
species: C. diphtheriae
biovar: Mitis
tox gene PCR: Positive
isolation year: 2017
country: Bangladesh
continent: Asia
travel history: Not documented
host: Human
source: Throat swab
accession number: SAMN11612661
sender: Mélanie Hennart, Institut Pasteur, France
curator: Auto Tagger
update history: 6 updates show details
date entered: 2022-07-25
datestamp: 2025-07-18

Sequence bin

method: Illumina + PacBio hybrid
contigs: 1
length: 2,474,411 bp
%GC: 53.55
Ns: 0
gaps: 0
loci tagged: 1,312

Show sequence bin

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_165_2_0_2_0_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL40
Clonal group: ClG453
Genetic cluster: GC42

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Prefix	Threshold	Matching isolates
0_0_165_2_0_2	8	2
0_0_165_2_0_2_0	4	2
0_0_165_2_0_2_0_0	2	2
0_0_165_2_0_2_0_0_0	1	1
0_0_165_2_0_2_0_0_0_0	0	1
0	1220	2380
0_0	1035	2162
0_0_165	500	35
0_0_165_2	55	10
0_0_165_2_0	25	10
0_0_165_2_0_2	8	2
0_0_165_2_0_2_0	4	2
0_0_165_2_0_2_0_0	2	2
0_0_165_2_0_2_0_0_0	1	1
0_0_165_2_0_2_0_0_0_0	0	1

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	21 (34 isolates)	SL: 453
Genomic_cluster	cgMLST	Single-linkage	25	experimental	21 (10 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	21 (34 isolates)	SL: 453
Genomic_cluster	cgMLST	Single-linkage	25	experimental	21 (10 isolates)

Schemes and loci

All loci
- Classical schemes
- Other schemes
  - PBP
  - spuA_island

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Tools

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