Full information on isolate SB5663 (id:4903)
Projects
This isolate is a member of the following project:
- Huynh et al 2020 Gut Microbes
- Collection of KpSC genomes studied in "Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors" (PMID 32404021, ACIP project)
Provenance/primary metadata
- id
- 4903
- isolate
- SB5663
- aliases
- a0324144; P242M
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 20 updates show details
- date entered
- 2017-02-24
- datestamp
- 2023-01-20
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2016
- city
- Pnom Penh
- country
- Cambodia
- continent
- Asia
- host
- pregnant woman
- source details
- Fecal sample
- infection
- carriage
- source lab
- Institut Pasteur du Cambodge
Publication (1)
- Huynh BT, Passet V, Rakotondrasoa A, Diallo T, Kerleguer A, Hennart M, Lauzanne A, Herindrainy P, Seck A, Bercion R, Borand L, Pardos de la Gandara M, Delarocque-Astagneau E, Guillemot D, Vray M, Garin B, Collard JM, Rodrigues C, Brisse S (2020). Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors. Gut Microbes 11:1287-1299
Sequence bin
- contigs
- 91
- total length
- 5,543,635 bp
- max length
- 1,037,702 bp
- mean length
- 60,920 bp
- N50
- 264,515
- L50
- 7
- N90
- 71,494
- L90
- 20
- N95
- 26,347
- L95
- 26
- %GC
- 57.18
- Ns
- 6
- gaps
- 1
- loci tagged
- 1,373
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 | 625 | 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
- 1
- resistance_score
- 1
- num_resistance_classes
- 7
- num_resistance_genes
- 7
- Yersiniabactin
- ybt 2; ICEKp1
- YbST
- 323-1LV
- CbST
- 0
- AbST
- 0
- Salmochelin
- iro 3 (truncated)
- SmST
- 7
- RmpADC
- rmp 3; ICEKp1
- RmST
- 32
- wzi
- wzi82
- K_locus
- unknown (KL23)
- K_type
- unknown (K23)
- K_locus_problems
- ?-
- K_locus_confidence
- Low
- K_locus_identity
- 99.94%
- K_locus_missing_genes
- KL23_09_wckU,KL23_10_wzy
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.45%
- Flq_acquired
- qnrS1
- Phe_acquired
- floR.v1*
- Sul_acquired
- sul2
- Tet_acquired
- tet(A).v1
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- LAP-2
- Bla_ESBL_acquired
- CTX-M-27
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- ybtS
- 8
- ybtX
- 7
- ybtQ
- 9
- ybtP
- 6
- ybtA
- 5
- irp2
- 13
- irp1
- 224
- ybtU
- 6
- ybtT
- 7
- ybtE
- 7
- fyuA
- 6
- iroB
- 6
- iroC
- 19-4%
- iroD
- 10
- iroN
- 5
- rmpA
- 11
- rmpD
- 5
- rmpC
- 6
Analysis performed: 2024-03-12; 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 (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) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: