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Full information on isolate 01A065 (id:3881)

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
Hennart et al. 2022_MBE
Reference Genomes for LINcodes (Table S9) (PMID: 35700230)

Provenance/primary metadata

id
3881
isolate
01A065
alias
SB1
sender
Camille Blin, Institut Pasteur
curator
Auto Tagger
update history
640 updates show details
date entered
2016-04-14
datestamp
2023-01-20
taxonomic designation
K. variicola subsp. variicola
phylogroup from ST
Kp3 (7 loci)
QC status
0000
isolation year
1997
city
Linz
country
Austria
continent
Europe
source type
Human
host
Human
source details
Blood
comments
Type alleles

Publications (3)

  • 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, 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:

Sequence bin

contigs
50
total length
5,426,844 bp
max length
548,528 bp
mean length
108,537 bp
N50
287,000
L50
7
N90
74,124
L90
23
N95
40,409
L95
28
%GC
57.58
Ns
0
gaps
0
loci tagged
3,767

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_S62961998

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Klebsiella variicola Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella variicola 100%

Analysis performed: 2022-12-01

Kleborate

species
Klebsiella variicola subsp. variicola
species_match
strong
virulence_score
0
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
wzi
wzi32
K_locus
KL31
K_type
K31
K_locus_problems
?-*
K_locus_confidence
Good
K_locus_identity
90.43%
K_locus_missing_genes
KL31_19_manB
O_locus
O3/O3a
O_type
O3/O3a
O_locus_problems
?-
O_locus_confidence
Good
O_locus_identity
99.17%
O_locus_missing_genes
O3/O3a_02_manB
Bla_chr
LEN-16^

Analysis performed: 2024-02-26; Kleborate v2.3.2

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups

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 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental19 (5 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental19 (5 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental19 (1 isolate)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental19 (1 isolate)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental19 (1 isolate)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental19 (1 isolate)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental19 (1 isolate)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental19 (1 isolate)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental19 (1 isolate)

Schemes and loci

Tools

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