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Full information on isolate SB610 (id:3887)

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
3887
isolate
SB610
sender
Camille Blin, Institut Pasteur
curator
Auto Tagger
update history
23 updates show details
date entered
2016-04-14
datestamp
2023-01-20
taxonomic designation
K. quasipneumoniae subsp. similipneumoniae
phylogroup from ST
Kp4 (7 loci)
QC status
0000
city
Utrecht
country
Netherlands
continent
Europe
source type
Environment
host
Environment
source details
Lake water
other source info
Collected by S. Brisse

Publications (2)

  • 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
  • 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
187
total length
5,704,513 bp
max length
287,315 bp
mean length
30,506 bp
N50
111,616
L50
17
N90
22,196
L90
57
N95
8,369
L95
77
%GC
56.89
Ns
0
gaps
0
loci tagged
3,649

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_S62961096

Analysis

rMLST species identification

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

Analysis performed: 2022-12-01

Kleborate

species
Klebsiella quasipneumoniae subsp. similipneumoniae
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
wzi545
K_locus
KL111
K_type
unknown (KL111)
K_locus_problems
*
K_locus_confidence
Very high
K_locus_identity
97.17%
O_locus
O12
O_type
O12
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
99.13%
Bla_chr
OKP-B-5*?

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_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental24 (1 isolate)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental24 (1 isolate)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental24 (1 isolate)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental24 (1 isolate)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental24 (1 isolate)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental24 (1 isolate)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental24 (1 isolate)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental24 (1 isolate)

Schemes and loci

Tools

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