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Full information on isolate VA01 (id:23)

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
23
isolate
VA01
alias
ASM25525v1
species
C. diphtheriae
tox gene PCR
Negative
isolation year
1999
city
Rio de Janeiro
country
Brazil
continent
South America
travel history
Not documented
host
Human
source
respiratory
infection or disease
diphtheria
accession number
CP003217
epidemic cluster
cryptic_5
sender
Melody Dazas, Institut Pasteur
curator
Auto Tagger
update history
1330 updates show details
embargo history
show details
date entered
2017-02-07
datestamp
2025-07-17

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
  • Trost E, Blom J, Soares Sde C, Huang IH, Al-Dilaimi A, Schröder J, Jaenicke S, Dorella FA, Rocha FS, Miyoshi A, Azevedo V, Schneider MP, Silva A, Camello TC, Sabbadini PS, Santos CS, Santos LS, Hirata R, Mattos-Guaraldi AL, Efstratiou A, Schmitt MP, Ton-That H, Tauch A (2012). Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia. J Bacteriol 194:3199-215

Sequence bin

method
Unknown
contigs
1
length
2,395,441 bp
%GC
53.44
Ns
0
gaps
0
loci tagged
1,381

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Similar isolates (determined by LIN codes)

Scheme
cgMLST
LIN code
0_0_42_0_1_0_0_0_0_0
Species
C. diphtheriae
Lineage
0_0
Sublineage
SL80
Clonal group
ClG80
Genetic cluster
GC91

Show all thresholds

PrefixThresholdMatching isolates
0_0_42_0_1_081
0_0_42_0_1_0_041
0_0_42_0_1_0_0_021
0_0_42_0_1_0_0_0_011
0_0_42_0_1_0_0_0_0_001
012202380
0_010352162
0_0_425004
0_0_42_0554
0_0_42_0_1252
0_0_42_0_1_081
0_0_42_0_1_0_041
0_0_42_0_1_0_0_021
0_0_42_0_1_0_0_0_011
0_0_42_0_1_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-linkage500experimental19 (4 isolates)
SL: 508
Genomic_clustercgMLSTSingle-linkage25experimental19 (3 isolates)
SublineagecgMLSTSingle-linkage500experimental19 (4 isolates)
SL: 508
Genomic_clustercgMLSTSingle-linkage25experimental19 (3 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

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