Full information on isolate G18584190 (id:15404)
Provenance/primary metadata
- id
- 15404
- isolate
- G18584190
- sender
- Iruka Okeke, University of Ibadan, Department of Pharmaceutical Microbiology, Iruka Okeke lab, Nigeria
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 10 updates show details
- date entered
- 2020-11-09
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- isolation year
- 2018
- city
- Ile-Ife
- country
- Nigeria
- continent
- Africa
- source type
- Human
- host
- Human
- source details
- Swab
- source lab
- OAU
- K type
- KL123
- K typing method
- Other
Sequence bin
- contigs
- 17
- total length
- 5,123,462 bp
- max length
- 2,234,328 bp
- mean length
- 301,381 bp
- N50
- 734,247
- L50
- 2
- N90
- 360,778
- L90
- 6
- N95
- 93,188
- L95
- 7
- %GC
- 57.70
- Ns
- 1081
- gaps
- 11
- loci tagged
- 708
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
- 0
- resistance_score
- 0
- num_resistance_classes
- 6
- num_resistance_genes
- 7
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi95
- K_locus
- KL123
- K_type
- unknown (KL123)
- K_locus_problems
- *
- K_locus_confidence
- High
- K_locus_identity
- 94.97%
- O_locus
- O5
- O_type
- O5
- O_locus_problems
- *
- O_locus_confidence
- High
- O_locus_identity
- 94.21%
- AGly_acquired
- aac(3)-IIa.v1;strA.v1*
- Flq_acquired
- qnrS1
- Sul_acquired
- sul2
- Tet_acquired
- tet(D)
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- TEM-1D.v1^
- Bla_chr
- SHV-1
Analysis performed: 2024-03-22; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_22_54_0_0_0_0_0_0
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_22_54_0_0 | 7 | 14 |
| 0_0_22_54_0_0_0 | 4 | 14 |
| 0_0_22_54_0_0_0_0 | 2 | 14 |
| 0_0_22_54_0_0_0_0_0 | 1 | 14 |
| 0_0_22_54_0_0_0_0_0_0 | 0 | 14 |
| 0 | 610 | 37942 |
| 0_0 | 585 | 37942 |
| 0_0_22 | 190 | 2094 |
| 0_0_22_54 | 43 | 15 |
| 0_0_22_54_0 | 10 | 14 |
| 0_0_22_54_0_0 | 7 | 14 |
| 0_0_22_54_0_0_0 | 4 | 14 |
| 0_0_22_54_0_0_0_0 | 2 | 14 |
| 0_0_22_54_0_0_0_0_0 | 1 | 14 |
| 0_0_22_54_0_0_0_0_0_0 | 0 | 14 |
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 (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 | 4 (589 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 552 (17 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 | 4 (589 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 552 (17 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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