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Full information on isolate YEM0039 (id:537)

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
537
isolate
YEM0039
alias
YE-NCPHL-310
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
ERR4332883
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Auto Tagger
update history
12 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
36
total length
2,471,797 bp
max length
441,853 bp
mean length
68,662 bp
N50
166,305
L50
5
N90
35,498
L90
16
N95
23,936
L95
20
%GC
53.56
Ns
0
gaps
0
loci tagged
1,302

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_209_6_0_0_0_0_0_0
Species
C. diphtheriae
Lineage
0_0
Sublineage
SL295
Clonal group
ClG83
Genetic cluster
GC622

Show all thresholds

PrefixThresholdMatching isolates
0_0_209_6_0_081
0_0_209_6_0_0_041
0_0_209_6_0_0_0_021
0_0_209_6_0_0_0_0_011
0_0_209_6_0_0_0_0_0_001
012202380
0_010352162
0_0_20950014
0_0_209_6553
0_0_209_6_0251
0_0_209_6_0_081
0_0_209_6_0_0_041
0_0_209_6_0_0_0_021
0_0_209_6_0_0_0_0_011
0_0_209_6_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-linkage500experimental41 (13 isolates)
SL: 295
SublineagecgMLSTSingle-linkage500experimental41 (13 isolates)
SL: 295
Genomic_clustercgMLSTSingle-linkage25experimental348 (1 isolate)

Schemes and loci

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