Full information on isolate SA1 (id:1511)
Projects
Provenance/primary metadata
- id
- 1511
- isolate
- SA1
- alias
- SB4021
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 731 updates show details
- date entered
- 2013-03-25
- datestamp
- 2023-01-20
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2008
- city
- Paris
- country
- France
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Blood
- infection
- Pneumonia
- source lab
- D. Decre, Hopital Saint-Antoine, AP-HP
- K type
- K2
Publications (3)
- Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S (2014). Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 20:1812-20
- 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
- Decré D, Verdet C, Emirian A, Le Gourrierec T, Petit JC, Offenstadt G, Maury E, Brisse S, Arlet G (2011). Emerging severe and fatal infections due to Klebsiella pneumoniae in two university hospitals in France. J Clin Microbiol 49:3012-4
Sequence bin
- contigs
- 67
- total length
- 5,492,681 bp
- max length
- 448,936 bp
- mean length
- 81,981 bp
- N50
- 250,254
- L50
- 9
- N90
- 49,315
- L90
- 30
- N95
- 32,169
- L95
- 37
- %GC
- 57.18
- Ns
- 0
- gaps
- 0
- loci tagged
- 4,073
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 | 626 | 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
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 4
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 22; ICEKp12
- YbST
- 13
- CbST
- 0
- Aerobactin
- iuc 1
- AbST
- 1
- Salmochelin
- iro 1
- SmST
- 1
- RmpADC
- rmp 1; KpVP-1
- RmST
- 26
- rmpA2
- rmpA2_4-34%
- wzi
- wzi2
- K_locus
- KL2
- K_type
- K2
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.94%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.46%
- Bla_chr
- SHV-1^
- ybtS
- 11
- ybtX
- 9
- ybtQ
- 11
- ybtP
- 8
- ybtA
- 1
- irp2
- 2
- irp1
- 2
- ybtU
- 8
- ybtT
- 9
- ybtE
- 8
- fyuA
- 8
- iucA
- 1
- iucB
- 1
- iucC
- 1
- iucD
- 1
- iutA
- 1
- iroB
- 1
- iroC
- 1
- iroD
- 1
- iroN
- 1
- rmpA
- 2
- rmpD
- 2
- rmpC
- 2
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 | 62 (61 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 69 (56 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 481 (5 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 1824 (2 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2238 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2794 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 3276 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4064 (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 | 62 (61 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 69 (56 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 481 (5 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 1824 (2 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2238 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 2794 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 3276 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4064 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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