Full information on isolate CIP 52.228 (id:1581)
Projects
This isolate is a member of the following project:
- Isolates Excluded (failed QC)
- KlebNET-GSP qc
Provenance/primary metadata
- id
- 1581
- isolate
- CIP 52.228
- aliases
- 2812/50; SB3259
- sender
- Suzanne Bialek, AP-HP
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 675 updates show details
- embargo history
- show details
- date entered
- 2013-04-11
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0100
- country
- Unknown
- host
- Unknown
- source lab
- Institut Pasteur, BBPE
- K type
- K23
- K typing method
- Antiserum
- comments
- K23 ref strain
Sequence bin
- method
- Illumina
- contigs
- 573
- total length
- 5,505,618 bp
- max length
- 88,574 bp
- mean length
- 9,609 bp
- N50
- 25,356
- L50
- 68
- N90
- 6,315
- L90
- 235
- N95
- 3,596
- L95
- 290
- %GC
- 56.88
- Ns
- 6961
- gaps
- 119
- loci tagged
- 2,457
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| 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 | 623 | 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
- QC_warnings
- ambiguous_bases
- virulence_score
- 2
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 17; ICEKp10
- YbST
- 289
- Colibactin
- clb 3
- CbST
- 55
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi169
- K_locus
- KL23
- K_type
- K23
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.96%
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.87%
- Bla_chr
- SHV-14^
- ybtS
- 6
- ybtX
- 15
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 11
- irp2
- 28
- irp1
- 26
- ybtU
- 2
- ybtT
- 11
- ybtE
- 4
- fyuA
- 2
- clbA
- 2
- clbB
- 9
- clbC
- 2
- clbD
- 2
- clbE
- 2
- clbF
- 2
- clbG
- 2
- clbH
- 8
- clbI
- 4
- clbL
- 2
- clbM
- 2
- clbN
- 2
- clbO
- 2
- clbP
- 2
- clbQ
- 2
Analysis performed: 2024-02-09; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_10_0_0_0_1_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL10009
- Clonal group
- CG10011
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 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 198 (21 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 734 (5 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 198 (21 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 734 (5 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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