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Full information on isolate YEM0044 (id:802)

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
802
isolate
YEM0044
alias
YE-NCPHL-563
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
ERR4332886
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Auto Tagger
update history
13 updates show details
date entered
2019-10-20
datestamp
2025-07-18

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
43
total length
2,474,039 bp
max length
316,089 bp
mean length
57,536 bp
N50
153,692
L50
6
N90
33,381
L90
17
N95
29,454
L95
21
%GC
53.56
Ns
0
gaps
0
loci tagged
1,301

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Corynebacterium diphtheriae Actinomycetota > Actinomycetes > Mycobacteriales > Corynebacteriaceae > Corynebacterium > Corynebacterium diphtheriae 100%

Analysis performed: 2025-06-05

Similar isolates (determined by LIN codes)

Scheme
cgMLST
LIN code
0_0_164_1_0_0_0_0_0_0
Species
C. diphtheriae
Lineage
0_0
Sublineage
SL447
Clonal group
ClG10143
Genetic cluster
GC205

Show all thresholds

PrefixThresholdMatching isolates
0_0_164_1_0_082
0_0_164_1_0_0_042
0_0_164_1_0_0_0_022
0_0_164_1_0_0_0_0_012
0_0_164_1_0_0_0_0_0_002
012202380
0_010352162
0_0_1645009
0_0_164_1552
0_0_164_1_0252
0_0_164_1_0_082
0_0_164_1_0_0_042
0_0_164_1_0_0_0_022
0_0_164_1_0_0_0_0_012
0_0_164_1_0_0_0_0_0_002

Similar isolates (determined by classification schemes)

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroupFields
SublineagecgMLSTSingle-linkage500experimental13 (8 isolates)
SL: 473
Genomic_clustercgMLSTSingle-linkage25experimental429 (2 isolates)
SublineagecgMLSTSingle-linkage500experimental13 (8 isolates)
SL: 473
Genomic_clustercgMLSTSingle-linkage25experimental429 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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