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Full information on isolate NTUH-K2044 (id:398)

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
398
isolate
NTUH-K2044
alias
SB3928
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Auto Tagger
update history
783 updates show details
date entered
2009-02-10
datestamp
2023-01-20
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
city
Taiwan
country
Taiwan
continent
Asia
source type
Human
host
Human
source details
Liver pus
infection
Liver abscess
source lab
Taiwan Univ. College of Medicine
K type
K1
comments
Type alleles
accession number
NC_012731, NC_006625

Publications (6)

  • 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
  • Blin C, Passet V, Touchon M, Rocha EPC, Brisse S (2017). Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae. Environ Microbiol 19:1881-1898
  • Brisse S, Fevre C, Passet V, Issenhuth-Jeanjean S, Tournebize R, Diancourt L, Grimont P (2009). Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS One 4:e4982
  • 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:
  • Wu KM, Li LH, Yan JJ, Tsao N, Liao TL, Tsai HC, Fung CP, Chen HJ, Liu YM, Wang JT, Fang CT, Chang SC, Shu HY, Liu TT, Chen YT, Shiau YR, Lauderdale TL, Su IJ, Kirby R, Tsai SF (2009). Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis. J Bacteriol 191:4492-501

Sequence bin

contigs
2
total length
5,472,672 bp
max length
5,248,520 bp
mean length
2,736,336 bp
N50
5,248,520
L50
1
N90
5,248,520
L90
1
N95
5,248,520
L95
1
%GC
57.37
Ns
0
gaps
0
loci tagged
4,068

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_S629629100

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
virulence_score
4
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
Yersiniabactin
ybt 2; ICEKp1
YbST
326
CbST
0
Aerobactin
iuc 1
AbST
1
Salmochelin
iro 1,iro 3
SmST
19,18
RmpADC
rmp 1; KpVP-1 (truncated),rmp 3; ICEKp1 (truncated)
RmST
26-1LV,119
rmpA2
rmpA2_3-47%
wzi
wzi1
K_locus
KL1
K_type
K1
K_locus_problems
none
K_locus_confidence
Perfect
K_locus_identity
100.00%
O_locus
O1/O2v2
O_type
O1
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
99.13%
Bla_chr
SHV-11.v1^
SHV_mutations
35Q
ybtS
9
ybtX
7
ybtQ
9
ybtP
6
ybtA
5
irp2
1
irp1
1
ybtU
6
ybtT
7
ybtE
7
fyuA
6
iucA
1
iucB
1
iucC
1
iucD
1
iutA
1
iroB
1,21
iroC
2,39
iroD
1,19
iroN
1,5
rmpA
54-47%,11
rmpD
2,38-86%
rmpC
2,6

Analysis performed: 2023-07-21; Kleborate v2.3.2

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_429_0_24_0_0_0_0_0

Show all thresholds

PrefixThresholdMatching isolates
0_0_429_0_24_073
0_0_429_0_24_0_043
0_0_429_0_24_0_0_022
0_0_429_0_24_0_0_0_012
0_0_429_0_24_0_0_0_0_002
061037874
0_058537874
0_0_429190408
0_0_429_043406
0_0_429_0_24105
0_0_429_0_24_073
0_0_429_0_24_0_043
0_0_429_0_24_0_0_022
0_0_429_0_24_0_0_0_012
0_0_429_0_24_0_0_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 (13440 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13419 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental6 (143 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (143 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental6 (3 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental6 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental6 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental6 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental6 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental6 (2 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13440 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13419 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental6 (143 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (143 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental6 (3 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental6 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental6 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental6 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental6 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental6 (2 isolates)

Schemes and loci

Tools

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