Full information on isolate SPARK_769_C1 (id:14316)
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
- 14316
- isolate
- SPARK_769_C1
- 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
- 18 updates show details
- date entered
- 2020-07-22
- datestamp
- 2024-05-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2017
- city
- Pavia province
- country
- Italy
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Skin
- other source info
- skin_swab
- source lab
- hospital_1
Sequence bin
- contigs
- 20
- total length
- 5,183,977 bp
- max length
- 1,376,493 bp
- mean length
- 259,199 bp
- N50
- 558,702
- L50
- 3
- N90
- 310,567
- L90
- 8
- N95
- 94,913
- L95
- 9
- %GC
- 57.68
- Ns
- 2
- gaps
- 2
- loci tagged
- 711
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 | 627 | 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 26; ICEKp18
- YbST
- 160-1LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi447
- K_locus
- unknown (KL124)
- K_type
- unknown (KL124)
- K_locus_problems
- ?-
- K_locus_confidence
- Low
- K_locus_identity
- 96.75%
- K_locus_missing_genes
- KL124_17_wclK
- O_locus
- OL101
- O_type
- unknown (OL101)
- O_locus_confidence
- High
- O_locus_identity
- 95.15%
- O_locus_missing_genes
- OL101_09_glycosylhydrolase
- Bla_chr
- SHV-1
- spurious_resistance_hits
- fosA7*?-0%
- ybtS
- 44
- ybtX
- 61
- ybtQ
- 58
- ybtP
- 65
- ybtA
- 40
- irp2
- 242
- irp1
- 140
- ybtU
- 45
- ybtT
- 38
- ybtE
- 63
- fyuA
- 66
Analysis performed: 2024-03-13; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_457_0_0_0_1_0_0_0
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 (13440 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13419 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 772 (7 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1267 (6 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13440 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13419 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 772 (7 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1267 (6 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: