Full information on isolate 09A323 (id:49)
Projects
Provenance/primary metadata
- id
- 49
- isolate
- 09A323
- alias
- SB164
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 28 updates show details
- date entered
- 2006-09-05
- datestamp
- 2022-11-03
- taxonomic designation
- K. quasipneumoniae subsp. similipneumoniae
- phylogroup from ST
- Kp4 (7 loci)
- QC status
- 0000
- isolation year
- 1997
- city
- Athens
- country
- Greece
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Blood
- source lab
- UMCU (Utrecht, NL)
- K type
- K35
Publications (3)
- Brisse S, Fevre C, Passet V, Issenhuth-Jeanjean S, Tournebize R, Diancourt L, Grimont P (2009). Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS One 4:e4982
- Diancourt L, Passet V, Verhoef J, Grimont PA, Brisse S (2005). Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol 43:4178-82
- 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
- 58
- total length
- 5,400,215 bp
- max length
- 1,578,843 bp
- mean length
- 93,108 bp
- N50
- 368,265
- L50
- 3
- N90
- 66,447
- L90
- 15
- N95
- 37,162
- L95
- 20
- %GC
- 57.78
- Ns
- 0
- gaps
- 0
- loci tagged
- 3,675
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 | 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
- 1
- resistance_score
- 1
- num_resistance_classes
- 4
- num_resistance_genes
- 5
- Yersiniabactin
- ybt 10; ICEKp4
- YbST
- 564
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi44
- K_locus
- KL123
- K_type
- unknown (KL123)
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.99%
- O_locus
- O3/O3a
- O_type
- O3/O3a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 95.98%
- AGly_acquired
- aac(3)-Ia*;aadA1.v1^
- Sul_acquired
- sul1
- Tet_acquired
- tet(D)
- Bla_ESBL_acquired
- SHV-5
- Bla_chr
- OKP-B-8
- SHV_mutations
- 238S;240K
- truncated_resistance_hits
- aac(6')-Ib10?-0%
- ybtS
- 3
- ybtX
- 12
- ybtQ
- 4
- ybtP
- 3
- ybtA
- 3
- irp2
- 85
- irp1
- 248
- ybtU
- 3
- ybtT
- 10
- ybtE
- 42
- fyuA
- 2
Analysis performed: 2023-07-21; 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 | 3 (9 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 3 (9 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 | 3 (9 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 3 (9 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 3 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 3 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 3 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 3 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 3 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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