Full information on isolate Kp13 (id:1761)
Projects
Provenance/primary metadata
- id
- 1761
- isolate
- Kp13
- alias
- SB4938
- sender
- Suzanne Bialek, AP-HP
- curator
- Auto Tagger
- update history
- 41 updates show details
- date entered
- 2014-01-02
- datestamp
- 2023-01-20
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2009
- country
- Brazil
- continent
- South America
- source type
- Human
- host
- Human
- source details
- Blood
- source lab
- Lab. Nacional de Computacao Cientifica, RJ
- resistance info
- KPC
- accession number
- CP003994-CP004000
Publications (2)
- Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022). A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Mol Biol Evol 39:
- Ramos PI, Picão RC, Almeida LG, Lima NC, Girardello R, Vivan AC, Xavier DE, Barcellos FG, Pelisson M, Vespero EC, Médigue C, Vasconcelos AT, Gales AC, Nicolás MF (2014). Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms. BMC Genomics 15:54
Sequence bin
- contigs
- 7
- total length
- 5,739,888 bp
- max length
- 5,307,003 bp
- mean length
- 819,984 bp
- N50
- 5,307,003
- L50
- 1
- N90
- 5,307,003
- L90
- 1
- N95
- 295,493
- L95
- 2
- %GC
- 56.79
- Ns
- 0
- gaps
- 0
- loci tagged
- 4,020
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: 2022-12-01
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 1
- resistance_score
- 3
- num_resistance_classes
- 9
- num_resistance_genes
- 15
- Yersiniabactin
- ybt 0; ICEKp5
- YbST
- 223
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi154
- K_locus
- KL107
- K_type
- unknown (KL107)
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.98%
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.37%
- AGly_acquired
- aac(6')-Ib'.v1*;aadA*;aadA2;rmtG;sat-2
- Phe_acquired
- cmlA4*
- Sul_acquired
- sul1;sul1;sul2
- Tmt_acquired
- dfrA15.v2*
- Bla_acquired
- OXA-9.v1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-2;SHV-12
- Bla_Carb_acquired
- KPC-2
- Bla_chr
- SHV-110
- SHV_mutations
- 156D;238S;240K;35Q;35Q
- Omp_mutations
- OmpK36GD
- Col_mutations
- MgrB-53%
- Flq_mutations
- GyrA-83F;GyrA-87N;ParC-80I
- ybtS
- 54
- ybtX
- 67
- ybtQ
- 68
- ybtP
- 73
- ybtA
- 1
- irp2
- 31
- irp1
- 31
- ybtU
- 51
- ybtT
- 1
- ybtE
- 84
- fyuA
- 88
Analysis performed: 2024-02-12; Kleborate v2.3.2
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 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 17 (23 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 17 (11 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 17 (5 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 17 (3 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 17 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 17 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 17 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 17 (2 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 17 (23 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 17 (11 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 17 (5 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 17 (3 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 17 (2 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 17 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 17 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 17 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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