Home About Us Contact What's New
Home>Organism>Corynebacterium cgMLST>Isolate information
Help

Full information on isolate YEM0035 (id:506)

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
506
isolate
YEM0035
alias
YE-NCPHL-213
species
C. diphtheriae
biovar
Mitis
tox gene PCR
Negative
isolation year
2018
city
Sanaa
country
Yemen
continent
Asia
travel history
Not documented
host
Human
accession number
ERR4332890
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
45
total length
2,379,680 bp
max length
247,369 bp
mean length
52,882 bp
N50
119,539
L50
8
N90
34,629
L90
22
N95
26,357
L95
26
%GC
53.57
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_107_0_0_0_0_0_0_0
Species
C. diphtheriae
Lineage
0_0
Sublineage
SL725
Clonal group
ClG725
Genetic cluster
GC193

Show all thresholds

PrefixThresholdMatching isolates
0_0_107_0_0_082
0_0_107_0_0_0_042
0_0_107_0_0_0_0_022
0_0_107_0_0_0_0_0_011
0_0_107_0_0_0_0_0_0_001
012202380
0_010352162
0_0_1075002
0_0_107_0552
0_0_107_0_0252
0_0_107_0_0_082
0_0_107_0_0_0_042
0_0_107_0_0_0_0_022
0_0_107_0_0_0_0_0_011
0_0_107_0_0_0_0_0_0_001

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-linkage500experimental196 (2 isolates)
SL: 725
Genomic_clustercgMLSTSingle-linkage25experimental326 (2 isolates)
SublineagecgMLSTSingle-linkage500experimental196 (2 isolates)
SL: 725
Genomic_clustercgMLSTSingle-linkage25experimental326 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Export:
Analysis: