Full information on isolate SPARK_1208_C2 (id:12970)
Projects
This isolate is a member of the following project:
- SPARK project
- Collection of KpSC genomes studied in "One Health or Three? Transmission modelling of Klebsiella isolates reveals ecological barriers to transmission between humans, animals and the environment" (BioRxiv,https://doi.org/10.1101/2021.08.05.455249)
Provenance/primary metadata
- id
- 12970
- isolate
- SPARK_1208_C2
- sender
- Edward Feil, Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom.
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 17 updates show details
- date entered
- 2020-07-22
- datestamp
- 2024-06-03
- 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
- contigs
- 76
- total length
- 5,426,264 bp
- max length
- 547,176 bp
- mean length
- 71,399 bp
- N50
- 307,882
- L50
- 7
- N90
- 45,870
- L90
- 22
- N95
- 26,970
- L95
- 30
- %GC
- 57.28
- Ns
- 407
- gaps
- 7
- loci tagged
- 715
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 | 628 | 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
- 0
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi7
- K_locus
- KL7
- K_type
- K7
- K_locus_problems
- ?
- K_locus_confidence
- Good
- 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
Analysis performed: 2024-03-13; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_10_1_0_1_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_127_10_1_0 | 7 | 3 |
| 0_0_127_10_1_0_1 | 4 | 2 |
| 0_0_127_10_1_0_1_0 | 2 | 2 |
| 0_0_127_10_1_0_1_0_0 | 1 | 2 |
| 0_0_127_10_1_0_1_0_0_0 | 0 | 2 |
| 0 | 610 | 37701 |
| 0_0 | 585 | 37701 |
| 0_0_127 | 190 | 105 |
| 0_0_127_10 | 43 | 20 |
| 0_0_127_10_1 | 10 | 4 |
| 0_0_127_10_1_0 | 7 | 3 |
| 0_0_127_10_1_0_1 | 4 | 2 |
| 0_0_127_10_1_0_1_0 | 2 | 2 |
| 0_0_127_10_1_0_1_0_0 | 1 | 2 |
| 0_0_127_10_1_0_1_0_0_0 | 0 | 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 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 95 (43 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1668 (4 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 95 (43 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1668 (4 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: