Full information on isolate 07A044 (id:1554)
Projects
Provenance/primary metadata
- id
- 1554
- isolate
- 07A044
- alias
- SB30
- sender
- Suzanne Bialek, AP-HP
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 1316 updates show details
- date entered
- 2013-04-11
- datestamp
- 2022-11-30
- taxonomic designation
- K. quasipneumoniae subsp. similipneumoniae
- phylogroup from ST
- Kp4 (7 loci)
- QC status
- 0002
- isolation year
- 1997
- city
- Freiburg
- country
- Germany
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Blood
- source lab
- UMCU (Utrecht, NL)
- comments
- Type alleles; type strain
Publications (3)
- 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
- Brisse S, Passet V, Grimont PAD (2014). Description of Klebsiella quasipneumoniae sp. nov., isolated from human infections, with two subspecies, Klebsiella quasipneumoniae subsp. quasipneumoniae subsp. nov. and Klebsiella quasipneumoniae subsp. similipneumoniae subsp. nov., and demonstration that Klebsiella singaporensis is a junior heterotypic synonym of Klebsiella variicola. Int J Syst Evol Microbiol 64:3146-3152
- 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
- 46
- total length
- 5,109,717 bp
- max length
- 488,431 bp
- mean length
- 111,081 bp
- N50
- 257,097
- L50
- 8
- N90
- 75,248
- L90
- 24
- N95
- 46,457
- L95
- 29
- %GC
- 58.20
- Ns
- 0
- gaps
- 0
- loci tagged
- 3,720
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC | %GC too high (fail threshold: 57.981) |
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 | 611 | 97 | |
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
- wzi164
- K_locus
- KL53
- K_type
- K53
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 98.04%
- O_locus
- O3/O3a
- O_type
- O3/O3a
- O_locus_problems
- ?
- O_locus_confidence
- Good
- O_locus_identity
- 95.98%
- Bla_chr
- OKP-B-1
Analysis performed: 2024-01-29; Kleborate v2.3.2
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 (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 | 14 (2 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 14 (2 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 14 (2 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 14 (2 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 14 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 14 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 14 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 14 (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 | 14 (2 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 14 (2 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 14 (2 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 14 (2 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 14 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 14 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 14 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 14 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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