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Full information on isolate SB6179 (id:8759)

Projects

This isolate is a member of the following projects:

Delgado-Blas et al. 2025
Collection of 336 isolates from different ecological sources (soil, WWTP, animals, clinical) recovered from July 2018 to July 2019. Preprint : Pangenome structure and ecological adaptation in the Klebsiella pneumoniae species complex: insights from a geographically and time limited multi-habitat study (doi: https://doi.org/10.64898/2025.12.11.693626)
Barbier et al_ApplEnvironMicrobiol_2020
Collection of KpSC genomes studied in "The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples" (PMID: 32005732)

Provenance/primary metadata

id
8759
isolate
SB6179
alias
MedVetKlebs65
sender
Elodie Barbier, Institut National de Recherche Agronomique (INRA) Dijon, France
curator
Carla Rodrigues, Institut Pasteur, France (E-mail: carla.parada-rodrigues@pasteur.fr)
update history
18 updates show details
date entered
2019-06-05
datestamp
2025-12-05
taxonomic designation
K. variicola subsp. variicola
QC status
0000
isolation year
2018
city
Bourgogne-Franche-Comté region
country
France
continent
Europe
source type
Environment
host
Environment
source details
roots
other source info
Organic vegetable farm-Sample 1 - roots
source lab
INRAE Dijon

Sequence bin

method
Illumina
contigs
48
total length
5,407,240 bp
max length
1,176,812 bp
mean length
112,651 bp
N50
360,448
L50
5
N90
103,297
L90
17
N95
60,176
L95
21
%GC
57.57
Ns
0
gaps
0
loci tagged
688

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_S62961898

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Klebsiella variicola Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella variicola 98%

Analysis performed: 2022-11-02

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
wzi198
K_locus
unknown (KL67)
K_type
unknown (K67)
K_locus_problems
?-*
K_locus_confidence
None
K_locus_identity
97.55%
K_locus_missing_genes
KL67_09_wckZ,KL67_10_wclH,KL67_11_wcqG,KL67_22_rmlD
O_locus
OL103
O_type
unknown (OL103)
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
98.91%
Bla_chr
LEN-13*

Analysis performed: 2025-05-14; Kleborate v2.3.2

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
1_0_196_0_0_0_0_0_0_0
Phylogroup
Kp3
Sublineage
SL10324
Clonal group
CG10739

Show all thresholds

PrefixThresholdMatching isolates
1_0_196_0_0_073
1_0_196_0_0_0_043
1_0_196_0_0_0_0_023
1_0_196_0_0_0_0_0_013
1_0_196_0_0_0_0_0_0_003
16101702
1_05851584
1_0_1961907
1_0_196_0433
1_0_196_0_0103
1_0_196_0_0_073
1_0_196_0_0_0_043
1_0_196_0_0_0_0_023
1_0_196_0_0_0_0_0_013
1_0_196_0_0_0_0_0_0_003

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 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental1022 (5 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental1723 (3 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental1022 (5 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental1723 (3 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

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