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Full information on isolate 12A476 (id:3885)

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
3885
isolate
12A476
alias
SB203
sender
Camille Blin, Institut Pasteur
curator
Auto Tagger
update history
28 updates show details
date entered
2016-04-14
datestamp
2023-01-20
taxonomic designation
K. quasipneumoniae subsp. similipneumoniae
phylogroup from ST
Mixed: Kp4 (6 loci), Kp4/Kp3 (1 locus)
QC status
0000
isolation year
1998
country
Netherlands
continent
Europe
source type
Human
host
Human
source details
Blood

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
71
total length
5,425,574 bp
max length
592,593 bp
mean length
76,417 bp
N50
346,454
L50
7
N90
67,146
L90
19
N95
26,211
L95
26
%GC
57.82
Ns
0
gaps
0
loci tagged
3,721

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_S62960996

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
2
num_resistance_genes
2
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
K_locus
KL61
K_type
K61
K_locus_problems
?-+*
K_locus_confidence
Good
K_locus_identity
95.83%
K_locus_missing_genes
KL61_17_manC,KL61_18_manB
O_locus
O3/O3a
O_type
O3/O3a
O_locus_problems
?-
O_locus_confidence
Good
O_locus_identity
96.07%
O_locus_missing_genes
O3/O3a_01_manC,O3/O3a_02_manB
AGly_acquired
aadA2
Sul_acquired
sul1
Bla_chr
OKP-B-3*

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-linkage190experimental22 (3 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental22 (3 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental22 (1 isolate)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental22 (1 isolate)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental22 (1 isolate)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental22 (1 isolate)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental22 (1 isolate)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental22 (1 isolate)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental22 (1 isolate)

Schemes and loci

Tools

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