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Full information on isolate YEM0019 (id:467)

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: 467
isolate: YEM0019
alias: YE-NCPHL-434
species: C. diphtheriae
biovar: Gravis
tox gene PCR: Positive
tox production Elek: Positive
isolation year: 2018
city: Saada
country: Yemen
continent: Asia
travel history: Not documented
host: Human
accession number: ERR4332859
sender: Sylvain Brisse, Institut Pasteur, Paris, France
curator: Auto Tagger
update history: 14 updates show details
date entered: 2019-10-20
datestamp: 2025-07-17

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: 49
total length: 2,402,292 bp
max length: 306,250 bp
mean length: 49,027 bp
N50: 119,370
L50: 6
N90: 28,207
L90: 21
N95: 19,200
L95: 26
%GC: 53.43
Ns: 0
gaps: 0
loci tagged: 1,307

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_18_0_0_1_0_0_1_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL384
Clonal group: ClG384
Genetic cluster: GC3

Show all thresholds Hide larger thresholds

Prefix	Threshold	Matching isolates
0_0_18_0_0_1	8	18
0_0_18_0_0_1_0	4	8
0_0_18_0_0_1_0_0	2	3
0_0_18_0_0_1_0_0_1	1	2
0_0_18_0_0_1_0_0_1_0	0	2
0	1220	2380
0_0	1035	2162
0_0_18	500	127
0_0_18_0	55	119
0_0_18_0_0	25	119
0_0_18_0_0_1	8	18
0_0_18_0_0_1_0	4	8
0_0_18_0_0_1_0_0	2	3
0_0_18_0_0_1_0_0_1	1	2
0_0_18_0_0_1_0_0_1_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	131 (119 isolates)	SL: 384
Genomic_cluster	cgMLST	Single-linkage	25	experimental	217 (115 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	131 (119 isolates)	SL: 384
Genomic_cluster	cgMLST	Single-linkage	25	experimental	217 (115 isolates)

Schemes and loci

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

Navigate and select schemes within tree to display allele designations

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