Full information on isolate SB1124 (id:3883)
Projects
Provenance/primary metadata
- id
- 3883
- isolate
- SB1124
- 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. quasipneumoniae
- phylogroup from ST
- Mixed: Kp2 (6 loci), Kp3 (1 locus)
- QC status
- 0000
- country
- Netherlands
- continent
- Europe
- source type
- Environment
- host
- Environment
- source details
- canal water
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
- 250
- total length
- 5,637,157 bp
- max length
- 332,919 bp
- mean length
- 22,549 bp
- N50
- 74,545
- L50
- 19
- N90
- 12,786
- L90
- 87
- N95
- 6,464
- L95
- 118
- %GC
- 57.41
- Ns
- 0
- gaps
- 0
- loci tagged
- 3,599
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 | 602 | 95 | |
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. quasipneumoniae
- 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
- wzi371
- K_locus
- KL138
- K_type
- unknown (KL138)
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 99.93%
- K_locus_missing_genes
- KL138_14_wzx
- O_locus
- unknown (OL102)
- O_type
- unknown (OL102)
- O_locus_problems
- -*
- O_locus_confidence
- None
- O_locus_identity
- 81.64%
- O_locus_missing_genes
- OL102_05_wbbL,OL102_06_rhamnan,OL102_07_wzm,OL102_08_wzt
- Omp_mutations
- OmpK35-0%
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 scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
|---|---|---|---|---|---|
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 548 (2 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 548 (2 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1176 (1 isolate) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 2138 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 2401 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2865 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3471 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 3987 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4903 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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