Full information on isolate SAKP01 (id:9639)
Projects
This isolate is a member of the following project:
- Rollin et al 2022_IJID
- Collection of K. pneumoniae genomes studied in "Spontaneous and postsurgical/traumatic Klebsiella pneumoniae meningitis: two distinct clinico-microbiological entities" (PMID: 34767984)
Provenance/primary metadata
- id
- 9639
- isolate
- SAKP01
- alias
- SA56
- sender
- Guillaume Rollin, Beaujon hospital, Paris, France
- curator
- Auto Tagger
- update history
- 9 updates show details
- date entered
- 2019-09-03
- datestamp
- 2023-01-21
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2011
- city
- Paris
- country
- France
- continent
- Europe
- host
- Human
- source details
- CSF
- infection
- Meningitis
- K type
- K1
Publication (1)
- Rollin G, Rossi B, Brisse S, Decré D, Leflon-Guibout V, Bert F, Hoffmann I, Decousser JW, Fantin B, Lefort A (2022). Spontaneous and postsurgical/traumatic Klebsiella pneumoniae meningitis: two distinct clinico-microbiological entities. Int J Infect Dis 114:185-191
Sequence bin
- contigs
- 381
- total length
- 5,894,075 bp
- max length
- 341,192 bp
- mean length
- 15,471 bp
- N50
- 203,744
- L50
- 11
- N90
- 26,221
- L90
- 41
- N95
- 3,659
- L95
- 79
- %GC
- 56.88
- Ns
- 0
- gaps
- 0
- loci tagged
- 794
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 | 629 | 100 |
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
- 5
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 1; ICEKp10
- YbST
- 47
- Colibactin
- clb 2
- CbST
- 29
- Aerobactin
- iuc 1
- AbST
- 1
- Salmochelin
- iro 1
- SmST
- 2
- RmpADC
- rmp unknown
- RmST
- 0
- wzi
- wzi1
- K_locus
- KL1
- K_type
- K1
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 100.00%
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.13%
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- ybtS
- 2
- ybtX
- 2
- ybtQ
- 2
- ybtP
- 2
- ybtA
- 2
- irp2
- 6
- irp1
- 6
- ybtU
- 2
- ybtT
- 2
- ybtE
- 2
- fyuA
- 2
- clbA
- 2
- clbB
- 2
- clbC
- 2
- clbD
- 2
- clbE
- 2
- clbF
- 2
- clbG
- 2
- clbH
- 3
- clbI
- 2
- clbL
- 2
- clbM
- 2
- clbN
- 2
- clbO
- 2
- clbP
- 2
- clbQ
- 2
- iucA
- 1
- iucB
- 1
- iucC
- 1
- iucD
- 1
- iutA
- 1
- iroB
- 1
- iroC
- 4
- iroD
- 1
- iroN
- 1
- rmpA
- 40*-54%
- rmpD
- 2
- spurious_virulence_hits
- rmpC_18*-0%;rmpC_24*-44%
Analysis performed: 2024-03-12; 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 | 6 (143 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 6 (143 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 | 6 (143 isolates) |
klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 6 (143 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: