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Full information on isolate FRC0405 (id:459)

Projects

This isolate is a member of the following projects:

ResistanceGenomics
Hennart et al. 247 isolates dataset
Hennart_diphtOscan_2023_OtherIsolates
Publicly-available genomes and isolates from the French NRC (2018-2021)
French Guiana 2016-2021 study
Isolates included in the French Guiana 2016-2021 study (Gaillet et al., Emerg Inf Dis, 2024, https://pubmed.ncbi.nlm.nih.gov/39043387/)
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
459
isolate
FRC0405
species
C. diphtheriae
biovar
Gravis
tox gene PCR
Negative
isolation year
2016
country
French Guiana
continent
South America
state or locality
French Guiana
travel history
Not documented
host
Human
source
Not documented
infection or disease
Not documented
accession number
ERS4330926
sender
Melody Dazas, Institut Pasteur
curator
Auto Tagger
update history
27 updates show details
date entered
2018-02-20
datestamp
2025-07-17

Publication (1)

  • Hennart M, Panunzi LG, Rodrigues C, Gaday Q, Baines SL, Barros-Pinkelnig M, Carmi-Leroy A, Dazas M, Wehenkel AM, Didelot X, Toubiana J, Badell E, Brisse S (2020). Population genomics and antimicrobial resistance in Corynebacterium diphtheriae. Genome Med 12:107

Sequence bin

method
Illumina
contigs
34
total length
2,407,978 bp
max length
454,701 bp
mean length
70,823 bp
N50
176,740
L50
4
N90
32,591
L90
15
N95
24,855
L95
19
%GC
53.54
Ns
0
gaps
0
loci tagged
1,372

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_52_0_0_0_0_0_0_0
Species
C. diphtheriae
Lineage
0_0
Sublineage
SL536
Clonal group
ClG536
Genetic cluster
GC226

Show all thresholds

PrefixThresholdMatching isolates
0_0_52_0_0_082
0_0_52_0_0_0_041
0_0_52_0_0_0_0_021
0_0_52_0_0_0_0_0_011
0_0_52_0_0_0_0_0_0_001
012202380
0_010352162
0_0_5250013
0_0_52_05511
0_0_52_0_0252
0_0_52_0_0_082
0_0_52_0_0_0_041
0_0_52_0_0_0_0_021
0_0_52_0_0_0_0_0_011
0_0_52_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-linkage500experimental178 (13 isolates)
SL: 536
Genomic_clustercgMLSTSingle-linkage25experimental295 (11 isolates)
SublineagecgMLSTSingle-linkage500experimental178 (13 isolates)
SL: 536
Genomic_clustercgMLSTSingle-linkage25experimental295 (11 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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