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Full information on isolate FRC0580 (id:864)

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: 864
isolate: FRC0580
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: 17 updates show details
date entered: 2019-03-08
datestamp: 2025-07-17

Sequence bin

method: Illumina
contigs: 40
total length: 2,481,603 bp
max length: 419,416 bp
mean length: 62,041 bp
N50: 246,448
L50: 4
N90: 39,717
L90: 16
N95: 23,462
L95: 20
%GC: 53.55
Ns: 7
gaps: 1
loci tagged: 1,399

Show sequence bin

Assembly checks

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

Similar isolates (determined by LIN codes)

Scheme: cgMLST
LIN code: 0_0_47_0_0_0_2_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL416
Clonal group: ClG416
Genetic cluster: GC14

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Prefix	Threshold	Matching isolates
0_0_47_0_0_0	8	26
0_0_47_0_0_0_2	4	13
0_0_47_0_0_0_2_0	2	1
0_0_47_0_0_0_2_0_0	1	1
0_0_47_0_0_0_2_0_0_0	0	1
0	1220	2380
0_0	1035	2162
0_0_47	500	27
0_0_47_0	55	26
0_0_47_0_0	25	26
0_0_47_0_0_0	8	26
0_0_47_0_0_0_2	4	13
0_0_47_0_0_0_2_0	2	1
0_0_47_0_0_0_2_0_0	1	1
0_0_47_0_0_0_2_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	82 (27 isolates)	SL: 416
Genomic_cluster	cgMLST	Single-linkage	25	experimental	108 (26 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	82 (27 isolates)	SL: 416
Genomic_cluster	cgMLST	Single-linkage	25	experimental	108 (26 isolates)

Schemes and loci

All loci

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Tools

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