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Full information on isolate ERR2173763 (id:15)

Projects

This isolate is a member of the following projects:

yemen2019
Yemen 2017-2020 outbreak
cgMLST set-up study
Isolates included in the cgMLST study (publicly-available genomes and some isolates from the French NRC)

Provenance/primary metadata

id
15
isolate
ERR2173763
alias
Cd_3
species
C. diphtheriae
isolation year
2015
city
Somalia
country
Somalia
continent
Africa
travel history
Not documented
host
Human
infection or disease
wound
accession number
PRJEB14914
epidemic cluster
Germany-Switzerland set 1
sender
Melody Dazas, Institut Pasteur
curator
Auto Tagger
update history
1318 updates show details
date entered
2018-05-29
datestamp
2022-08-09
outbreak or sporadic
Cluster

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

contigs
48
total length
2,456,475 bp
max length
315,785 bp
mean length
51,177 bp
N50
133,271
L50
6
N90
31,380
L90
18
N95
25,882
L95
23
%GC
53.55
Ns
100
gaps
1
loci tagged
1,374

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: 2024-01-25

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-linkage25experimental13 (3 isolates)
SublineagecgMLSTSingle-linkage500experimental13 (8 isolates)
SL: 473
Genomic_clustercgMLSTSingle-linkage25experimental13 (3 isolates)

Schemes and loci

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