Full information on isolate Kp_8890 (id:22143)
Provenance/primary metadata
- id
- 22143
- isolate
- Kp_8890
- sender
- Muhammad Asif, KEMU
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 8 updates show details
- date entered
- 2022-07-04
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2018
- city
- Lahore
- country
- Pakistan
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Blood
- infection
- Bactermia
- source lab
- Mayo Hospital Lahore
- K type
- K_17
- K typing method
- Full sequencing of CPS cluster
Sequence bin
- method
- Illumina
- contigs
- 50
- total length
- 5,426,150 bp
- max length
- 517,441 bp
- mean length
- 108,523 bp
- N50
- 355,986
- L50
- 7
- N90
- 166,854
- L90
- 14
- N95
- 86,660
- L95
- 17
- %GC
- 57.27
- Ns
- 0
- gaps
- 0
- loci tagged
- 719
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: 2022-12-06
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 1
- resistance_score
- 1
- num_resistance_classes
- 7
- num_resistance_genes
- 11
- Yersiniabactin
- ybt 13; ICEKp2
- YbST
- 304-2LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi137
- K_locus
- KL17
- K_type
- K17
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.98%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.02%
- AGly_acquired
- aac(6')-Ib-cr.v2;aph3-Ia.v1^;strA.v1^;strB.v1*
- Flq_acquired
- qnrB1.v2^
- Phe_acquired
- CatB4.v1
- Sul_acquired
- sul2*
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- OXA-1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1^
- ybtS
- 6
- ybtX
- 4
- ybtQ
- 20
- ybtP
- 61
- ybtA
- 1
- irp2
- 253*
- irp1
- 283*
- ybtU
- 2
- ybtT
- 76
- ybtE
- 4
- fyuA
- 2
Analysis performed: 2024-07-22; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_89_0_12_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL870
- Clonal group
- CG870
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 | 244 (22 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 367 (22 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 | 244 (22 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 367 (22 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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