Full information on isolate SB610 (id:3887)
Projects
Provenance/primary metadata
- id
- 3887
- isolate
- SB610
- sender
- Camille Blin, Institut Pasteur
- curator
- Auto Tagger
- update history
- 23 updates show details
- date entered
- 2016-04-14
- datestamp
- 2023-01-20
- taxonomic designation
- K. quasipneumoniae subsp. similipneumoniae
- phylogroup from ST
- Kp4 (7 loci)
- QC status
- 0000
- city
- Utrecht
- country
- Netherlands
- continent
- Europe
- source type
- Environment
- host
- Environment
- source details
- Lake water
- other source info
- Collected by S. Brisse
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
- method
- Illumina
- contigs
- 187
- total length
- 5,704,513 bp
- max length
- 287,315 bp
- mean length
- 30,506 bp
- N50
- 111,616
- L50
- 17
- N90
- 22,196
- L90
- 57
- N95
- 8,369
- L95
- 77
- %GC
- 56.89
- Ns
- 0
- gaps
- 0
- loci tagged
- 3,649
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 | 53 | 100 | |
| scgMLST629_S | 629 | 610 | 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. similipneumoniae
- 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
- wzi545
- K_locus
- KL111
- K_type
- unknown (KL111)
- K_locus_problems
- *
- K_locus_confidence
- Very high
- K_locus_identity
- 97.17%
- O_locus
- O12
- O_type
- O12
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.13%
- Bla_chr
- OKP-B-5*?
Analysis performed: 2025-05-12; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 2_1_38_0_0_0_0_0_0_0
- Phylogroup
- Kp4
- Sublineage
- SL2276
- Clonal group
- CG2276
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 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_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 | 24 (1 isolate) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 24 (1 isolate) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 24 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 24 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 24 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 24 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 24 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 24 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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