Full information on isolate GCA_002406605.1 (id:47604)
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
- 47604
- isolate
- GCA_002406605.1
- alias
- C6
- 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
- 2023-03-23
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- isolation year
- 0
- city
- Unknown
- country
- India
- continent
- Asia
- source type
- Unknown
- host
- Unknown
- source details
- Unknown
- accession number
- SAMN07689048
Sequence bin
- contigs
- 114
- total length
- 5,518,071 bp
- max length
- 354,961 bp
- mean length
- 48,405 bp
- N50
- 177,892
- L50
- 11
- N90
- 41,866
- L90
- 35
- N95
- 24,997
- L95
- 44
- %GC
- 57.08
- Ns
- 0
- gaps
- 0
- loci tagged
- 678
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 | 599 | 95 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 4
- resistance_score
- 1
- num_resistance_classes
- 9
- num_resistance_genes
- 10
- Yersiniabactin
- ybt 14; ICEKp5 (truncated)
- YbST
- 376-1LV
- CbST
- 0
- Aerobactin
- iuc 5
- AbST
- 61-3LV
- SmST
- 0
- RmST
- 0
- wzi
- wzi104
- K_locus
- KL51
- K_type
- K51
- K_locus_confidence
- High
- K_locus_identity
- 99.39%
- K_locus_missing_genes
- KL51_14_wcoZ
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.44%
- AGly_acquired
- aac(6')-Ib;aadA2^
- MLS_acquired
- ermB.v1*;mphA
- Phe_acquired
- catA1^
- Rif_acquired
- arr-2
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA12
- Bla_acquired
- TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-30%;OmpK36TD
- Flq_mutations
- GyrA-83I;ParC-80I
- truncated_resistance_hits
- OXA-232?-0%
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 8*-36%
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
- iucA
- 29
- iucB
- 17
- iucC
- 35
- iucD
- 35
- iutA
- 61
Analysis performed: 2024-04-17; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_0_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 (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 | 48 (88 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (82 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 50 (69 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 127 (66 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 141 (42 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 651 (16 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 722 (14 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 | 48 (88 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (82 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 50 (69 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 127 (66 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 141 (42 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 651 (16 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 722 (14 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 836 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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