Full information on isolate DSM 30104T (id:1546)

Projects

This isolate is a member of the following projects:

Public isolates: This project contains the isolates that should be publicly available through the public access database.
published_genomes: All isolates with published genome imported in BIGSdb, and validated for scgMLST_S study
Bialek et al 2014_EID: 167 isolates from Bialek et al. in which the scgMLST-634 scheme was defined (PMID: 25341126)
Hennart et al. 2022_MBE: Reference Genomes for LINcodes (Table S9) (PMID: 35700230)

Provenance/primary metadata

id: 1546
isolate: DSM 30104T
aliases: ATCC 13883T; SB132
sender: Suzanne Bialek, AP-HP
curator: Auto Tagger
update history: 106 updates show details
date entered: 2013-04-11
datestamp: 2023-01-20
taxonomic designation: K. pneumoniae
phylogroup from ST: Mixed: Kp1 (6 loci), Outgroup (1 locus)
QC status: 0000
country: Unknown
source type: Human
host: Human
source details: Blood
duplicate number: 2
accession number: AJJI01

Publications (4)

Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S (2014). Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 20:1812-20
Brisse S, Passet V, Grimont PAD (2014). Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola. Int J Syst Evol Microbiol 64:3146-3152
Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022). A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Mol Biol Evol 39:
Lee JH, Cheon IS, Shim BS, Kim DW, Kim SW, Chun J, Song M (2012). Draft genome sequence of Klebsiella pneumoniae subsp. pneumoniae DSM 30104T. J Bacteriol 194:5722-3

Sequence bin

contigs: 22
total length: 5,234,536 bp
max length: 1,148,365 bp
mean length: 237,934 bp
N50: 459,638
L50: 4
N90: 190,809
L90: 10
N95: 72,389
L95: 13
%GC: 57.32
Ns: 7
gaps: 3
loci tagged: 3,972

Show sequence bin

Assembly checks

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

Annotation quality metrics

Scheme completion

Scheme	Scheme loci	Designated loci	Annotation
Scheme	Scheme loci	Designated loci	Score	Status
MLST	7	7	100
Ribosomal MLST	53	53	100
scgMLST629_S	629	625	99

Analysis

rMLST species identification

Rank	Taxon	Taxonomy	Support	Matches
SPECIES	Klebsiella pneumoniae	Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae	100%

Analysis performed: 2022-12-01

Kleborate

species: Klebsiella pneumoniae
species_match: strong
QC_warnings: ambiguous_bases
virulence_score: 2
resistance_score: 0
num_resistance_classes: 0
num_resistance_genes: 0
YbST: 0
Colibactin: clb 1 (incomplete)
CbST: 59-6LV
AbST: 0
SmST: 0
RmST: 0
wzi: wzi3
K_locus: KL3
K_type: K3
K_locus_problems: none
K_locus_confidence: Very high
K_locus_identity: 99.60%
O_locus: O1/O2v1
O_type: O1
O_locus_problems: none
O_locus_confidence: Very high
O_locus_identity: 98.28%
Bla_chr: SHV-1^
clbA: 4
clbB: 6
clbC: 1
clbD: 3
clbE: 1
clbF: 3
clbG: 1
clbH: 6
clbI: 3

Analysis performed: 2024-01-29; Kleborate v2.3.2

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
klebs_species_v1.0	scgMLST629_S	Single-linkage	610	experimental	1 (13436 isolates)
klebs_subspecies_v1.0	scgMLST629_S	Single-linkage	585	experimental	1 (13415 isolates)
klebs_sublineage_v1.0	scgMLST629_S	Single-linkage	190	experimental	13 (10 isolates)
klebs_clonalgroup_v1.0	scgMLST629_S	Single-linkage	43	experimental	13 (10 isolates)
klebs_threshold10_v1.0	scgMLST629_S	Single-linkage	10	experimental	13 (7 isolates)
klebs_threshold7_v1.0	scgMLST629_S	Single-linkage	7	experimental	13 (7 isolates)
klebs_threshold4_v1.0	scgMLST629_S	Single-linkage	4	experimental	13 (7 isolates)
klebs_threshold2_v1.0	scgMLST629_S	Single-linkage	2	experimental	13 (2 isolates)
klebs_threshold1_v1.0	scgMLST629_S	Single-linkage	1	experimental	13 (2 isolates)
klebs_threshold0_v1.0	scgMLST629_S	Single-linkage	0	experimental	13 (2 isolates)
klebs_species_v1.0	scgMLST629_S	Single-linkage	610	experimental	1 (13436 isolates)
klebs_subspecies_v1.0	scgMLST629_S	Single-linkage	585	experimental	1 (13415 isolates)
klebs_sublineage_v1.0	scgMLST629_S	Single-linkage	190	experimental	13 (10 isolates)
klebs_clonalgroup_v1.0	scgMLST629_S	Single-linkage	43	experimental	13 (10 isolates)
klebs_threshold10_v1.0	scgMLST629_S	Single-linkage	10	experimental	13 (7 isolates)
klebs_threshold7_v1.0	scgMLST629_S	Single-linkage	7	experimental	13 (7 isolates)
klebs_threshold4_v1.0	scgMLST629_S	Single-linkage	4	experimental	13 (7 isolates)
klebs_threshold2_v1.0	scgMLST629_S	Single-linkage	2	experimental	13 (2 isolates)
klebs_threshold1_v1.0	scgMLST629_S	Single-linkage	1	experimental	13 (2 isolates)
klebs_threshold0_v1.0	scgMLST629_S	Single-linkage	0	experimental	13 (2 isolates)

Schemes and loci

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Tools

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