Full information on isolate SB5615 (id:4661)
Projects
Provenance/primary metadata
- id
- 4661
- isolate
- SB5615
- alias
- 1381
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 24 updates show details
- date entered
- 2016-11-18
- datestamp
- 2024-05-03
- taxonomic designation
- K. quasipneumoniae subsp. similipneumoniae
- phylogroup from ST
- Kp4 (7 loci)
- QC status
- 0002
- isolation year
- 2016
- country
- Madagascar
- continent
- Africa
- host
- pregnant woman
- source details
- Fecal sample
- infection
- carriage
- source lab
- Institut Pasteur of Madagascar
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
- 30
- total length
- 5,113,756 bp
- max length
- 704,934 bp
- mean length
- 170,459 bp
- N50
- 364,932
- L50
- 6
- N90
- 98,943
- L90
- 15
- N95
- 65,589
- L95
- 18
- %GC
- 58.20
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,356
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC | %GC too high (fail threshold: 57.981) |
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 | 610 | 96 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella quasipneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella quasipneumoniae | 100% |
Analysis performed: 2022-11-02
Kleborate
- species
- Klebsiella quasipneumoniae subsp. similipneumoniae
- species_match
- strong
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi533
- K_locus
- unknown (KL107)
- K_type
- unknown (KL107)
- K_locus_problems
- ?-+*
- K_locus_confidence
- None
- K_locus_identity
- 84.56%
- K_locus_missing_genes
- KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10
- O_locus
- O5
- O_type
- O5
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 96.14%
- Bla_chr
- OKP-B-2
Analysis performed: 2024-03-12; Kleborate v2.3.2
Schemes and loci
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Tools
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