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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
108 updates show details
date entered
2013-04-11
datestamp
2025-05-29
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

method
Unknown
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
6,630

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST5353100
scgMLST629_S62962599
Kpn_cgMLST2752265896

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
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: 2025-03-14; Kleborate v2.3.2

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_421_0_1_0_1_0_0_0
Phylogroup
Kp1
Sublineage
SL3
Clonal group
CG3

Show all thresholds

PrefixThresholdMatching isolates
0_0_421_0_1_0728
0_0_421_0_1_0_142
0_0_421_0_1_0_1_022
0_0_421_0_1_0_1_0_012
0_0_421_0_1_0_1_0_0_002
061041312
0_058541312
0_0_42119031
0_0_421_04331
0_0_421_0_11028
0_0_421_0_1_0728
0_0_421_0_1_0_142
0_0_421_0_1_0_1_022
0_0_421_0_1_0_1_0_012
0_0_421_0_1_0_1_0_0_002

Similar isolates (determined by classification schemes)

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

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental13 (19 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental13 (19 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental13 (16 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental13 (16 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental13 (16 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental13 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental13 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental13 (2 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental13 (19 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental13 (19 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental13 (16 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental13 (16 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental13 (16 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental13 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental13 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental13 (2 isolates)

Schemes and loci

Tools

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