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Full information on isolate 342 (id:1512)

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
1512
isolate
342
alias
Kp342
sender
Sylvain Brisse, Institut Pasteur, Paris, France
curator
Auto Tagger
update history
761 updates show details
date entered
2013-03-26
datestamp
2023-01-20
taxonomic designation
K. variicola subsp. variicola
phylogroup from ST
Kp3 (7 loci)
QC status
0000
country
USA
continent
North America
source type
Food
host
Maize
source details
Unknown
other source info
Reference endophytic strain
source lab
Triplett, E.
duplicate number
3
comments
Type alleles
accession number
NC_011281, NC_011282, NC_011283

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
  • Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LF, Krogfelt KA, Struve C, Triplett EW, Methé BA (2008). Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet 4:e1000141
  • 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
3
total length
5,920,257 bp
max length
5,641,239 bp
mean length
1,973,419 bp
N50
5,641,239
L50
1
N90
5,641,239
L90
1
N95
5,641,239
L95
1
%GC
56.87
Ns
0
gaps
0
loci tagged
3,780

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_S62961397

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
wzi159
K_locus
KL30
K_type
K30
K_locus_problems
*
K_locus_confidence
Very high
K_locus_identity
95.40%
O_locus
O3/O3a
O_type
O3/O3a
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
98.72%
Bla_chr
LEN-22*;LEN-22*

Analysis performed: 2023-07-21; 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 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-linkage190experimental12 (3 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental12 (3 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental12 (2 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental12 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental12 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental12 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental12 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental12 (2 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental12 (3 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental12 (3 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental12 (2 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental12 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental12 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental12 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental12 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental12 (2 isolates)

Schemes and loci

Tools

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