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

Full information on isolate ERR2173762 (id:5)

Projects

This isolate is a member of the following projects:

cgMLST set-up study
Isolates included in the cgMLST study (Guglielmini et al. J CLin Microbiol 2021 https://pubmed.ncbi.nlm.nih.gov/34524891/)
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
5
isolate
ERR2173762
alias
Cd_2
species
C. diphtheriae
isolation year
2015
country
Eritrea
continent
Africa
travel history
Not documented
host
Human
infection or disease
wound
accession number
PRJEB14914
sender
Melody Dazas, Institut Pasteur
curator
Mélanie Hennart, Institut Pasteur, France (E-mail: melanie.hennart@orange.fr)
update history
1312 updates show details
embargo history
show details
date entered
2018-05-29
datestamp
2023-01-24

Publications (2)

  • Guglielmini J, Hennart M, Badell E, Toubiana J, Criscuolo A, Brisse S (2021). Genomic Epidemiology and Strain Taxonomy of Corynebacterium diphtheriae. J Clin Microbiol 59:e0158121
  • Meinel DM, Kuehl R, Zbinden R, Boskova V, Garzoni C, Fadini D, Dolina M, Blümel B, Weibel T, Tschudin-Sutter S, Widmer AF, Bielicki JA, Dierig A, Heininger U, Konrad R, Berger A, Hinic V, Goldenberger D, Blaich A, Stadler T, Battegay M, Sing A, Egli A (2016). Outbreak investigation for toxigenic Corynebacterium diphtheriae wound infections in refugees from Northeast Africa and Syria in Switzerland and Germany by whole genome sequencing. Clin Microbiol Infect 22:1003.e1-1003.e8

Sequence bin

method
Unknown
contigs
33
total length
2,403,059 bp
max length
497,452 bp
mean length
72,820 bp
N50
202,991
L50
4
N90
28,076
L90
14
N95
19,507
L95
19
%GC
53.38
Ns
199
gaps
2
loci tagged
1,377

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_63_0_0_0_0_0_0_0
Species
C. diphtheriae
Lineage
0_0
Sublineage
SL504
Clonal group
ClG504
Genetic cluster
GC366

Show all thresholds

PrefixThresholdMatching isolates
0_0_63_0_0_081
0_0_63_0_0_0_041
0_0_63_0_0_0_0_021
0_0_63_0_0_0_0_0_011
0_0_63_0_0_0_0_0_0_001
012202380
0_010352162
0_0_635001
0_0_63_0551
0_0_63_0_0251
0_0_63_0_0_081
0_0_63_0_0_0_041
0_0_63_0_0_0_0_021
0_0_63_0_0_0_0_0_011
0_0_63_0_0_0_0_0_0_001

Similar isolates (determined by classification schemes)

No similar isolates at any threshold. Show groups

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Export:
Analysis: