Full information on isolate 18A069 (id:1555)

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: 1555
isolate: 18A069
alias: SB59
sender: Suzanne Bialek, AP-HP
curator: Auto Tagger
update history: 1312 updates show details
date entered: 2013-04-11
datestamp: 2023-01-20
taxonomic designation: K. quasipneumoniae subsp. quasipneumoniae
phylogroup from ST: Kp2 (7 loci)
QC status: 0000
isolation year: 1997
city: Barcelona
country: Spain
continent: Europe
source type: Human
host: Human
source details: Blood
source lab: UMCU (Utrecht, NL)
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: 1
length: 5,435,233 bp
%GC: 57.86
Ns: 47500
gaps: 475
loci tagged: 3,590

Show sequence bin

Assembly checks

Check	Status	Warn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Annotation quality metrics

Scheme completion

Scheme	Scheme loci	Designated loci	Annotation
Scheme	Scheme loci	Designated loci	Score	Status
MLST	7	7	100
Ribosomal MLST	53	53	100
scgMLST629_S	629	604	96

Analysis

rMLST species identification

Rank	Taxon	Taxonomy	Support	Matches
SPECIES	Klebsiella quasipneumoniae	Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella quasipneumoniae	100%

Analysis performed: 2022-12-01

Kleborate

species: Klebsiella quasipneumoniae subsp. quasipneumoniae
species_match: strong
QC_warnings: ambiguous_bases
virulence_score: 0
resistance_score: 0
num_resistance_classes: 2
num_resistance_genes: 2
YbST: 0
CbST: 0
AbST: 0
SmST: 0
RmST: 0
wzi: wzi165
K_locus: KL10
K_type: K10
K_locus_problems: *
K_locus_confidence: Very high
K_locus_identity: 95.16%
O_locus: O3/O3a
O_type: O3/O3a
O_locus_problems: ?
O_locus_confidence: Good
O_locus_identity: 95.87%
AGly_acquired: aadA^
Sul_acquired: sul1
Bla_chr: OKP-A-2

Analysis performed: 2024-01-29; 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 scheme	Underlying scheme	Clustering method	Mismatch threshold	Status	Group
klebs_species_v1.0	scgMLST629_S	Single-linkage	610	experimental	1 (13436 isolates)
klebs_subspecies_v1.0	scgMLST629_S	Single-linkage	585	experimental	1 (13415 isolates)
klebs_sublineage_v1.0	scgMLST629_S	Single-linkage	190	experimental	15 (2 isolates)
klebs_clonalgroup_v1.0	scgMLST629_S	Single-linkage	43	experimental	15 (2 isolates)
klebs_threshold10_v1.0	scgMLST629_S	Single-linkage	10	experimental	15 (2 isolates)
klebs_threshold7_v1.0	scgMLST629_S	Single-linkage	7	experimental	15 (2 isolates)
klebs_threshold4_v1.0	scgMLST629_S	Single-linkage	4	experimental	15 (2 isolates)
klebs_threshold2_v1.0	scgMLST629_S	Single-linkage	2	experimental	15 (2 isolates)
klebs_threshold1_v1.0	scgMLST629_S	Single-linkage	1	experimental	15 (2 isolates)
klebs_threshold0_v1.0	scgMLST629_S	Single-linkage	0	experimental	15 (2 isolates)
klebs_species_v1.0	scgMLST629_S	Single-linkage	610	experimental	1 (13436 isolates)
klebs_subspecies_v1.0	scgMLST629_S	Single-linkage	585	experimental	1 (13415 isolates)
klebs_sublineage_v1.0	scgMLST629_S	Single-linkage	190	experimental	15 (2 isolates)
klebs_clonalgroup_v1.0	scgMLST629_S	Single-linkage	43	experimental	15 (2 isolates)
klebs_threshold10_v1.0	scgMLST629_S	Single-linkage	10	experimental	15 (2 isolates)
klebs_threshold7_v1.0	scgMLST629_S	Single-linkage	7	experimental	15 (2 isolates)
klebs_threshold4_v1.0	scgMLST629_S	Single-linkage	4	experimental	15 (2 isolates)
klebs_threshold2_v1.0	scgMLST629_S	Single-linkage	2	experimental	15 (2 isolates)
klebs_threshold1_v1.0	scgMLST629_S	Single-linkage	1	experimental	15 (2 isolates)
klebs_threshold0_v1.0	scgMLST629_S	Single-linkage	0	experimental	15 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

Export:

Third party:

Analysis: