Full information on isolate T7-106 (id:14567)
Projects
This isolate is a member of the following project:
- Raffelsberger et al 2021_GutMicrobes
- Collection of KpSC genomes studied in "Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity" (PMID: 34182896, T7 Klebsiella project)
Provenance/primary metadata
- id
- 14567
- isolate
- T7-106
- sender
- Carla Rodrigues, Institut Pasteur
- curator
- Auto Tagger
- update history
- 9 updates show details
- date entered
- 2020-09-16
- datestamp
- 2023-01-22
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2015
- country
- Norway
- continent
- Europe
- host
- Homo sapiens
- source details
- Faeces
Publication (1)
- Raffelsberger N, Hetland MAK, Svendsen K, Småbrekke L, Löhr IH, Andreassen LLE, Brisse S, Holt KE, Sundsfjord A, Samuelsen Ø, Gravningen K (2021). Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity. Gut Microbes 13:1939599
Sequence bin
- contigs
- 65
- total length
- 5,099,496 bp
- max length
- 453,309 bp
- mean length
- 78,454 bp
- N50
- 280,759
- L50
- 8
- N90
- 48,464
- L90
- 25
- N95
- 34,195
- L95
- 31
- %GC
- 57.72
- Ns
- 0
- gaps
- 0
- loci tagged
- 697
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: 2022-11-02
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- 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
- wzi100
- K_locus
- unknown (KL10)
- K_type
- unknown (K10)
- K_locus_problems
- ?-+
- K_locus_confidence
- Low
- K_locus_identity
- 96.81%
- K_locus_missing_genes
- KL10_18_manC,KL10_19_manB
- O_locus
- O3/O3a
- O_type
- O3/O3a
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 97.94%
- O_locus_missing_genes
- O3/O3a_01_manC,O3/O3a_02_manB
- Bla_chr
- SHV-164*
Analysis performed: 2024-03-13; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_46_19_0_0_0_0_0_0
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
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 (13481 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 52 (57 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13481 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13460 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 52 (57 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2533 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: