Full information on isolate SB6478 (id:9533)

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)

id: 9533
isolate: SB6478
alias: MVK-03E163
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: 17 updates show details
date entered: 2019-08-08
datestamp: 2025-12-05
taxonomic designation: K. pneumoniae
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 26 - basil roots
source lab: INRAE Dijon

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	629	100

Rank	Taxon	Taxonomy	Support	Matches
SPECIES	Klebsiella pneumoniae	Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae	98%

Analysis performed: 2022-11-02

species: Klebsiella pneumoniae
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
K_locus: unknown (KL107)
K_type: unknown (KL107)
K_locus_problems: ?-
K_locus_confidence: None
K_locus_identity: 91.19%
K_locus_missing_genes: KL107_03_wzi,KL107_04_wza,KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_11_gnd,KL107_13,KL107_14,KL107_15
O_locus: unknown (OL102)
O_type: unknown (OL102)
O_locus_problems: ?-+*
O_locus_confidence: None
O_locus_identity: 83.83%
O_locus_missing_genes: OL102_02_rfbA,OL102_03_rfbD,OL102_04_rfbC,OL102_05_wbbL,OL102_06_rhamnan,OL102_07_wzm,OL102_08_wzt
Bla_chr: SHV-11.v1^
SHV_mutations: 35Q

Analysis performed: 2024-03-12; Kleborate v2.3.2

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 (16003 isolates)
klebs_subspecies_v1.0	scgMLST629_S	Single-linkage	585	experimental	1 (15951 isolates)
klebs_sublineage_v1.0	scgMLST629_S	Single-linkage	190	experimental	1558 (11 isolates)
klebs_clonalgroup_v1.0	scgMLST629_S	Single-linkage	43	experimental	2621 (11 isolates)
klebs_species_v1.0	scgMLST629_S	Single-linkage	610	experimental	1 (16003 isolates)
klebs_subspecies_v1.0	scgMLST629_S	Single-linkage	585	experimental	1 (15951 isolates)
klebs_sublineage_v1.0	scgMLST629_S	Single-linkage	190	experimental	1558 (11 isolates)
klebs_clonalgroup_v1.0	scgMLST629_S	Single-linkage	43	experimental	2621 (11 isolates)

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