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Full information on isolate CIP107542 (id:559)

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: 559
isolate: CIP107542
species: C. diphtheriae
biovar: Mitis
tox gene PCR: Negative
tox production Elek: Negative
isolation year: 1998
city: Moskva
country: Russia
continent: Asia
travel history: Not documented
host: Human
accession number: ERS4330806
sender: Melody Dazas, Institut Pasteur
curator: Auto Tagger
update history: 14 updates show details
date entered: 2018-02-20
datestamp: 2025-07-18

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: 32
total length: 2,368,491 bp
max length: 282,482 bp
mean length: 74,016 bp
N50: 164,481
L50: 6
N90: 40,810
L90: 15
N95: 33,227
L95: 18
%GC: 53.53
Ns: 0
gaps: 0
loci tagged: 1,394

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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_168_0_0_1_0_0_0_0
Species: C. diphtheriae
Lineage: 0_0
Sublineage: SL26
Clonal group: ClG26
Genetic cluster: GC4

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Prefix	Threshold	Matching isolates
0_0_168_0_0_1	8	1
0_0_168_0_0_1_0	4	1
0_0_168_0_0_1_0_0	2	1
0_0_168_0_0_1_0_0_0	1	1
0_0_168_0_0_1_0_0_0_0	0	1
0	1220	2380
0_0	1035	2162
0_0_168	500	50
0_0_168_0	55	49
0_0_168_0_0	25	49
0_0_168_0_0_1	8	1
0_0_168_0_0_1_0	4	1
0_0_168_0_0_1_0_0	2	1
0_0_168_0_0_1_0_0_0	1	1
0_0_168_0_0_1_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	4 (50 isolates)	SL: 26
Genomic_cluster	cgMLST	Single-linkage	25	experimental	4 (49 isolates)
Sublineage	cgMLST	Single-linkage	500	experimental	4 (50 isolates)	SL: 26
Genomic_cluster	cgMLST	Single-linkage	25	experimental	4 (49 isolates)

Schemes and loci

All loci

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