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Full information on isolate YEM0010 (id:402)

Projects

This isolate is a member of the following projects:

yemen2019: Yemen 2017-2020 outbreak
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: 402
isolate: YEM0010
alias: YE-NCPHL-260
species: C. diphtheriae
biovar: Mitis
tox gene PCR: Positive
tox production Elek: Positive
isolation year: 2018
city: Sanaa
country: Yemen
continent: Asia
travel history: Not documented
host: Human
accession number: ERR4332894
sender: Sylvain Brisse, Institut Pasteur, Paris, France
curator: Auto Tagger
update history: 14 updates show details
date entered: 2019-08-30
datestamp: 2022-08-09

Publication (1)

Badell E, Alharazi A, Criscuolo A, Almoayed KAA, Lefrancq N, Bouchez V, Guglielmini J, Hennart M, Carmi-Leroy A, Zidane N, Pascal-Perrigault M, Lebreton M, Martini H, Salje H, Toubiana J, Dureab F, Dhabaan G, Brisse S (2021). Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study. Lancet Microbe 2:e386-e396

Sequence bin

method: Illumina
contigs: 25
total length: 2,453,425 bp
max length: 434,284 bp
mean length: 98,137 bp
N50: 178,692
L50: 5
N90: 55,379
L90: 14
N95: 49,389
L95: 16
%GC: 53.77
Ns: 0
gaps: 0
loci tagged: 1,299

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_5_0_2_1_0_0_0_0_0
Species: C. diphtheriae
Lineage: 0_5
Sublineage: SL100
Clonal group: ClG100
Genetic cluster: GC119

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Prefix	Threshold	Matching isolates
0_5_0_2_1_0	8	3
0_5_0_2_1_0_0	4	3
0_5_0_2_1_0_0_0	2	3
0_5_0_2_1_0_0_0_0	1	2
0_5_0_2_1_0_0_0_0_0	0	2
0	1220	2380
0_5	1035	13
0_5_0	500	13
0_5_0_2	55	4
0_5_0_2_1	25	3
0_5_0_2_1_0	8	3
0_5_0_2_1_0_0	4	3
0_5_0_2_1_0_0_0	2	3
0_5_0_2_1_0_0_0_0	1	2
0_5_0_2_1_0_0_0_0_0	0	2

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	155 (7 isolates)	SL: 100
Genomic_cluster	cgMLST	Single-linkage	25	experimental	254 (3 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	155 (7 isolates)	SL: 100
Genomic_cluster	cgMLST	Single-linkage	25	experimental	254 (3 isolates)

Schemes and loci

All loci
- Classical schemes
- Other schemes
  - PBP
  - tox

Navigate and select schemes within tree to display allele designations

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