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Full information on isolate FRC0599 (id:868)

Projects

This isolate is a member of the following projects:

New Caledonia 2015-2019 study: Isolates included in the New Caledonia study (Tessier et al., 2023, Microbiol Spectr, https://pubmed.ncbi.nlm.nih.gov/37042786/)
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: 868
isolate: FRC0599
species: C. diphtheriae
biovar: Gravis
tox gene PCR: Negative
isolation year: 2018
country: New Caledonia
continent: Oceania
state or locality: New Caledonia
travel history: Not documented
host: Human
source: Cutaneous and soft tissue
infection or disease: Cutaneous and soft tissue infection
other source info: Wound
sender: Sylvain Brisse, Institut Pasteur, Paris, France
curator: Auto Tagger
update history: 19 updates show details
date entered: 2019-03-08
datestamp: 2025-07-18

Sequence bin

method: Illumina
contigs: 50
total length: 2,352,533 bp
max length: 269,804 bp
mean length: 47,051 bp
N50: 126,381
L50: 6
N90: 32,788
L90: 22
N95: 21,353
L95: 27
%GC: 53.54
Ns: 0
gaps: 0
loci tagged: 1,346

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Assembly checks

Check	Status	Warn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Analysis

rMLST species identification

Rank	Taxon	Taxonomy	Support	Matches
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_14_2_0_0_0_0_0_0_0
Species: C. diphtheriae
Lineage: 0_14
Sublineage: SL533
Clonal group: ClG533
Genetic cluster: GC58

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Prefix	Threshold	Matching isolates
0_14_2_0_0_0	8	1
0_14_2_0_0_0_0	4	1
0_14_2_0_0_0_0_0	2	1
0_14_2_0_0_0_0_0_0	1	1
0_14_2_0_0_0_0_0_0_0	0	1
0	1220	2380
0_14	1035	40
0_14_2	500	7
0_14_2_0	55	7
0_14_2_0_0	25	7
0_14_2_0_0_0	8	1
0_14_2_0_0_0_0	4	1
0_14_2_0_0_0_0_0	2	1
0_14_2_0_0_0_0_0_0	1	1
0_14_2_0_0_0_0_0_0_0	0	1

Similar isolates (determined by classification schemes)

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification scheme	Underlying scheme	Clustering method	Mismatch threshold	Status	Group	Fields
Sublineage	cgMLST	Single-linkage	500	experimental	193 (7 isolates)	SL: 533
Genomic_cluster	cgMLST	Single-linkage	25	experimental	322 (7 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	193 (7 isolates)	SL: 533
Genomic_cluster	cgMLST	Single-linkage	25	experimental	322 (7 isolates)

Schemes and loci

All loci

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Tools

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