Full information on isolate GCA_003443835.1 (id:52993)
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
- 52993
- isolate
- GCA_003443835.1
- alias
- L22
- sender
- Mélanie Hennart, Institut Pasteur
- curator
- Auto Tagger
- update history
- 4 updates show details
- date entered
- 2023-03-23
- datestamp
- 2023-04-14
- taxonomic designation
- K. quasipneumoniae subsp. similipneumoniae
- phylogroup from ST
- Kp4 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- China
- continent
- Asia
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMN09708445
Sequence bin
- contigs
- 6
- total length
- 5,631,032 bp
- max length
- 5,133,312 bp
- mean length
- 938,506 bp
- N50
- 5,133,312
- L50
- 1
- N90
- 5,133,312
- L90
- 1
- N95
- 95,314
- L95
- 3
- %GC
- 57.20
- Ns
- 0
- gaps
- 0
- loci tagged
- 667
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 quasipneumoniae subsp. similipneumoniae
- species_match
- strong
- virulence_score
- 3
- resistance_score
- 1
- num_resistance_classes
- 9
- num_resistance_genes
- 13
- YbST
- 0
- CbST
- 0
- Aerobactin
- iuc 1
- AbST
- 1
- Salmochelin
- iro 1
- SmST
- 1
- RmpADC
- rmp 1; KpVP-1
- RmST
- 26
- rmpA2
- rmpA2_6-60%
- wzi
- wzi233
- K_locus
- KL1
- K_type
- K1
- K_locus_problems
- *
- K_locus_confidence
- High
- K_locus_identity
- 94.25%
- O_locus
- O3/O3a
- O_type
- O3/O3a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 96.00%
- AGly_acquired
- aac(6')-Ib-cr.v2;aadA16*;ant(4')-Ib
- Fcyn_acquired
- fosD
- Flq_acquired
- qnrB6^;qnrS1
- MLS_acquired
- cfrA
- Rif_acquired
- arr-3
- Sul_acquired
- sul1;sul1^
- Tmt_acquired
- dfrA27
- Bla_acquired
- TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- OKP-B-9*
- Omp_mutations
- OmpK35-69%
- iucA
- 1
- iucB
- 1
- iucC
- 1
- iucD
- 1
- iutA
- 1
- iroB
- 1
- iroC
- 1
- iroD
- 1
- iroN
- 1
- rmpA
- 2
- rmpD
- 2
- rmpC
- 2
Analysis performed: 2024-04-26; 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 | 42 (9 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 42 (5 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 | 42 (9 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 42 (5 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 1897 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 2152 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2609 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3209 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 3723 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4618 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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