Full information on isolate BD-DU (id:1521)
Projects
Provenance/primary metadata
- id
- 1521
- isolate
- BD-DU
- alias
- SB4565
- sender
- Suzanne Bialek, AP-HP
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 721 updates show details
- date entered
- 2013-03-29
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0100
- isolation year
- 2011
- city
- Bordeaux
- country
- France
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Liver pus
- infection
- Liver abscess
- source lab
- B. De Barbeyrac, Bordeaux
- K type
- K1
- K typing method
- PCR
Publication (1)
- Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S (2014). Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 20:1812-20
Sequence bin
- contigs
- 774
- total length
- 5,542,863 bp
- max length
- 66,850 bp
- mean length
- 7,162 bp
- N50
- 11,826
- L50
- 143
- N90
- 3,458
- L90
- 474
- N95
- 2,360
- L95
- 569
- %GC
- 57.20
- Ns
- 0
- gaps
- 0
- loci tagged
- 3,756
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| Assembly size | ||
| Minimum N50 | N50 too low (warn threshold: 20,000) | |
| %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 | 572 | 90 | |
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
- virulence_score
- 5
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 1; ICEKp10 (incomplete) (truncated)
- YbST
- 342-4LV
- Colibactin
- clb 2 (incomplete)
- CbST
- 27-2LV
- Aerobactin
- iuc 1 (incomplete)
- AbST
- 1-2LV
- Salmochelin
- iro 1 (incomplete)
- SmST
- 2-1LV
- RmpADC
- rmp 1; KpVP-1
- RmST
- 26
- rmpA2
- rmpA2_5-54%
- wzi
- wzi1
- K_locus
- KL1
- K_type
- K1
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.98%
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.12%
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- Omp_mutations
- OmpK35-82%
- ybtS
- 2
- ybtX
- 2*-0%
- ybtQ
- 8
- ybtA
- 2
- ybtU
- 2
- ybtT
- 2
- ybtE
- 2
- fyuA
- 2
- clbA
- 2
- clbB
- 2
- clbC
- 3
- clbD
- 2
- clbE
- 2
- clbF
- 2
- clbG
- 2
- clbH
- 3
- clbI
- 2
- clbL
- 2
- clbM
- 2
- clbN
- 2
- clbP
- 2
- clbQ
- 2
- iucA
- 1
- iucC
- 1*
- iucD
- 1
- iutA
- 1
- iroC
- 4
- iroD
- 1
- iroN
- 1
- rmpA
- 2
- rmpD
- 2
- rmpC
- 2
- spurious_virulence_hits
- irp2_179*-0%;irp1_245*-0%;irp1_245*-42%;ybtP_2*-0%;irp2_220*-45%;clbO_13*-0%;iucB_1*-0%;iroB_1*-75%
Analysis performed: 2024-01-29; Kleborate v2.3.2
Schemes and loci
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