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Full information on isolate YEM0040 (id:539)

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
539
isolate
YEM0040
alias
YE-NCPHL-200
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
ERR4332885
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Auto Tagger
update history
12 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
48
total length
2,527,753 bp
max length
315,726 bp
mean length
52,662 bp
N50
150,389
L50
6
N90
31,497
L90
22
N95
23,981
L95
26
%GC
53.56
Ns
0
gaps
0
loci tagged
1,303

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_0_0_0_0_0_0_0
Species
C. diphtheriae
Lineage
0_0
Sublineage
SL447
Clonal group
ClG447
Genetic cluster
GC535

Show all thresholds

PrefixThresholdMatching isolates
0_0_164_0_0_081
0_0_164_0_0_0_041
0_0_164_0_0_0_0_021
0_0_164_0_0_0_0_0_011
0_0_164_0_0_0_0_0_0_001
012202380
0_010352162
0_0_1645009
0_0_164_0554
0_0_164_0_0251
0_0_164_0_0_081
0_0_164_0_0_0_041
0_0_164_0_0_0_0_021
0_0_164_0_0_0_0_0_011
0_0_164_0_0_0_0_0_0_001

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups

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
SublineagecgMLSTSingle-linkage500experimental13 (8 isolates)
SL: 473
Genomic_clustercgMLSTSingle-linkage25experimental350 (1 isolate)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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