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Full information on isolate CIP107560 (id:580)

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)
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: 580
isolate: CIP107560
species: C. diphtheriae
biovar: Gravis
tox gene PCR: Positive
tox production Elek: Positive
isolation year: 1993
city: Sankt-Peterbourg
country: Russia
continent: Asia
travel history: Not documented
host: Human
accession number: ERS4330820
sender: Melody Dazas, Institut Pasteur
curator: Auto Tagger
update history: 17 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: 27
total length: 2,440,262 bp
max length: 329,230 bp
mean length: 90,381 bp
N50: 179,058
L50: 5
N90: 45,781
L90: 13
N95: 29,881
L95: 16
%GC: 53.48
Ns: 10
gaps: 1
loci tagged: 1,399

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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_0_0_0_7_0_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL8
Clonal group: ClG8
Genetic cluster: GC29

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Prefix	Threshold	Matching isolates
0_0_0_0_0_7	8	1
0_0_0_0_0_7_0	4	1
0_0_0_0_0_7_0_0	2	1
0_0_0_0_0_7_0_0_0	1	1
0_0_0_0_0_7_0_0_0_0	0	1
0	1220	2380
0_0	1035	2162
0_0_0	500	88
0_0_0_0	55	88
0_0_0_0_0	25	13
0_0_0_0_0_7	8	1
0_0_0_0_0_7_0	4	1
0_0_0_0_0_7_0_0	2	1
0_0_0_0_0_7_0_0_0	1	1
0_0_0_0_0_7_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	1 (88 isolates)	SL: 8
Genomic_cluster	cgMLST	Single-linkage	25	experimental	1 (13 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	1 (88 isolates)	SL: 8
Genomic_cluster	cgMLST	Single-linkage	25	experimental	1 (13 isolates)

Schemes and loci

All loci

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Tools

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