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Full information on isolate YEM0051 (id:822)

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: 822
isolate: YEM0051
alias: YE-NCPHL-460
species: C. diphtheriae
biovar: Gravis
tox gene PCR: Negative
isolation year: 2018
city: Sanaa
country: Yemen
continent: Asia
travel history: Not documented
host: Human
accession number: ERR4332884
sender: Sylvain Brisse, Institut Pasteur, Paris, France
curator: Auto Tagger
update history: 13 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: 38
total length: 2,472,351 bp
max length: 441,859 bp
mean length: 65,062 bp
N50: 135,015
L50: 5
N90: 38,511
L90: 17
N95: 21,538
L95: 21
%GC: 53.50
Ns: 0
gaps: 0
loci tagged: 1,300

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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_209_6_2_0_0_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL295
Clonal group: ClG83
Genetic cluster: GC834

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Prefix	Threshold	Matching isolates
0_0_209_6_2_0	8	1
0_0_209_6_2_0_0	4	1
0_0_209_6_2_0_0_0	2	1
0_0_209_6_2_0_0_0_0	1	1
0_0_209_6_2_0_0_0_0_0	0	1
0	1220	2380
0_0	1035	2162
0_0_209	500	14
0_0_209_6	55	3
0_0_209_6_2	25	1
0_0_209_6_2_0	8	1
0_0_209_6_2_0_0	4	1
0_0_209_6_2_0_0_0	2	1
0_0_209_6_2_0_0_0_0	1	1
0_0_209_6_2_0_0_0_0_0	0	1

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups Hide single groups

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	41 (13 isolates)	SL: 295
Sublineage	cgMLST	Single-linkage	500	experimental	41 (13 isolates)	SL: 295
Genomic_cluster	cgMLST	Single-linkage	25	experimental	439 (1 isolate)

Schemes and loci

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

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