Full information on isolate SB6548 (id:9583)
Projects
This isolate is a member of the following project:
- 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)
Provenance/primary metadata
- id
- 9583
- isolate
- SB6548
- alias
- MVK-03F071
- 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
- 20 updates show details
- embargo history
- 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
- Other
- host
- Environment
- source details
- WWTP
- source lab
- INRAE Dijon
Sequence bin
- method
- Illumina
- contigs
- 167
- total length
- 5,164,419 bp
- max length
- 255,879 bp
- mean length
- 30,925 bp
- N50
- 72,051
- L50
- 22
- N90
- 22,886
- L90
- 69
- N95
- 14,459
- L95
- 84
- %GC
- 57.61
- Ns
- 0
- gaps
- 0
- loci tagged
- 713
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 | |
|---|---|---|---|---|
| Score | Status | |||
| MLST | 7 | 7 | 100 | |
| Ribosomal MLST | 53 | 51 | 96 | |
| scgMLST629_S | 629 | 628 | 99 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2022-11-02
Kaptive
| Database | Best match locus | Best match type | Match confidence | Problems | Identity | Coverage | Length discrepancy | Expected genes in locus | Missing expected genes | Other genes in locus | Other genes in locus, details | Expected genes outside locus | Expected genes outside locus, details | Other genes outside locus | Other genes outside locus, details | Truncated genes, details | Extra genes, details |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Klebsiella K locus | KL7 | K7 | Typeable | ?5- | 99.40% | 51.48% | n/a | 10 / 20 (50.00%) | KL7_08_wckC;KL7_12_wclS;KL7_11_wckD;KL7_07_wcuE;KL7_13_wcuJ;KL7_16_wcaJ;KL7_10_wzy;KL7_14_wzx;KL7_15_wbaZ;KL7_09_wcuC | 0 | 0 / 20 (0.00%) | 3 | KL150_19_gmd,98.50%,100.00%;KL40_05_rfaG,97.59%,87.37%,partial;KL40_05_rfaG,100.00%,11.32%,partial | ||||
| Klebsiella O locus | OL2α.1 | O1αβ,2α | Typeable | ?2 | 99.43% | 99.67% | n/a | 7 / 7 (100.00%) | 0 | 0 / 7 (0.00%) | 2 | OL3γ_01_manC,99.79%,100.00%;OL3γ_02_manB,99.55%,97.39% | Extra_genes_wbbYZ_02_wbbY,99.86%,100.00%;Extra_genes_wbbYZ_01_wbbZ,99.26%,100.00% |
Klebsiella K locus
Klebsiella O locus
Analysis performed: 2026-03-13; Kaptive Version 3.1.0. Citation: Stanton et al. (2025) bioRxiv 2025.02.05.636613.
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- virulence_score
- 0
- Bla_chr
- SHV-1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Ciprofloxacin_prediction
- wildtype S
- Ciprofloxacin_profile_support
- 90.99% S (N=5168/5680)
- Ciprofloxacin_profile
- 0^ QRDR, 0 PMQR, 0 aac(6`)-Ib-cr
- Ciprofloxacin_MIC_prediction
- 0.25 mg/L [0.25-0.25]
- wzi
- wzi7
- K_locus
- KL7
- K_type
- K7
- K_locus_confidence
- Typeable
- K_locus_problems
- ?5-
- K_locus_identity
- 99.40%
- K_Missing_expected_genes
- KL7_14_wzx;KL7_16_wcaJ;KL7_09_wcuC;KL7_13_wcuJ;KL7_10_wzy;KL7_07_wcuE;KL7_08_wckC;KL7_11_wckD;KL7_12_wclS;KL7_15_wbaZ
- O_locus
- OL2α.1
- O_type
- O1αβ,2α
- O_locus_confidence
- Typeable
- O_locus_problems
- ?2
- O_locus_identity
- 99.43%
Analysis performed: 2026-03-14; Kleborate v3.2.4
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_2_1_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL6
- Clonal group
- CG10246
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 (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 | 95 (53 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 332 (7 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 | 95 (53 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 332 (7 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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