Full information on isolate GCA_002269905.1 (id:53617)
Projects
This isolate is a member of the following project:
- Hennart_et_al_2022_full_collection
- Collection of genomes from the paper "A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains" | PMID: 35700230
Provenance/primary metadata
- id
- 53617
- isolate
- GCA_002269905.1
- alias
- A5
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 4 updates show details
- date entered
- 2023-04-03
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- USA
- continent
- North America
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMN06445923
Sequence bin
- contigs
- 329
- total length
- 5,554,133 bp
- max length
- 266,343 bp
- mean length
- 16,882 bp
- N50
- 86,237
- L50
- 22
- N90
- 17,054
- L90
- 73
- N95
- 9,273
- L95
- 94
- %GC
- 57.12
- Ns
- 0
- gaps
- 0
- loci tagged
- 672
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 | 607 | 96 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 0
- resistance_score
- 2
- num_resistance_classes
- 6
- num_resistance_genes
- 12
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi82
- K_locus
- KL23
- K_type
- K23
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.94%
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.43%
- O_locus_missing_genes
- O1/O2v2_03_wbbM
- AGly_acquired
- aac(6')-Ib'.v1*;aadA*;ant(2'')-Ia;strA.v1^;strB.v1
- Flq_acquired
- qnrA1
- Sul_acquired
- sul1;sul2
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- OXA-9.v1;TEM-1D.v1^
- Bla_Carb_acquired
- KPC-3
- truncated_resistance_hits
- SHV-105*?-0%
Analysis performed: 2024-04-25; Kleborate v2.3.2
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 (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 | 4 (588 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 63 (13 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 | 4 (588 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 63 (13 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 315 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 343 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 395 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 460 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 504 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 573 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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