Full information on isolate SPARK_2063_C1 (id:13559)
Projects
This isolate is a member of the following project:
- Thorpe et al. 2022_NatMicrobiol
- SPARK project - collection of KpSC genomes studied in "A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings" (PMID: 36411354; https://doi.org/10.1038/s41564-022-01263-0)
Provenance/primary metadata
- id
- 13559
- isolate
- SPARK_2063_C1
- sender
- Edward Feil, Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom.
- curator
- Auto Tagger
- update history
- 19 updates show details
- date entered
- 2020-07-22
- datestamp
- 2025-05-29
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2018
- city
- Pavia province
- country
- Italy
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Faeces
- source lab
- hospital_1
Sequence bin
- method
- Unknown
- contigs
- 65
- total length
- 5,565,694 bp
- max length
- 439,359 bp
- mean length
- 85,627 bp
- N50
- 215,219
- L50
- 10
- N90
- 55,947
- L90
- 25
- N95
- 34,927
- L95
- 31
- %GC
- 57.14
- Ns
- 1
- gaps
- 1
- loci tagged
- 3,469
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 | |
| Kpn_cgMLST | 2752 | 2739 | 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
- 1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 376
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi7
- K_locus
- KL7
- K_type
- K7
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 98.54%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.62%
- Bla_chr
- SHV-1
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 8
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
Analysis performed: 2024-03-13; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_8_12_0_1_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL6
- Clonal group
- CG6
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_127_8_12_0 | 7 | 1 |
| 0_0_127_8_12_0_1 | 4 | 1 |
| 0_0_127_8_12_0_1_0 | 2 | 1 |
| 0_0_127_8_12_0_1_0_0 | 1 | 1 |
| 0_0_127_8_12_0_1_0_0_0 | 0 | 1 |
| 0 | 610 | 41312 |
| 0_0 | 585 | 41312 |
| 0_0_127 | 190 | 121 |
| 0_0_127_8 | 43 | 33 |
| 0_0_127_8_12 | 10 | 1 |
| 0_0_127_8_12_0 | 7 | 1 |
| 0_0_127_8_12_0_1 | 4 | 1 |
| 0_0_127_8_12_0_1_0 | 2 | 1 |
| 0_0_127_8_12_0_1_0_0 | 1 | 1 |
| 0_0_127_8_12_0_1_0_0_0 | 0 | 1 |
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 | 95 (53 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 304 (25 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 | 95 (53 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 304 (25 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: