Full information on isolate A3021 (id:396)
Projects
Provenance/primary metadata
- id
- 396
- isolate
- A3021
- aliases
- A3021; SB3926
- sender
- Sylvain Brisse, Institut Pasteur, Paris, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 727 updates show details
- date entered
- 2009-02-10
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0100
- city
- Taiwan
- country
- Taiwan
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Liver pus
- infection
- Liver abscess
- source lab
- Taiwan Univ. College of Medicine
- K type
- K1
Publications (2)
- 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
- Brisse S, Fevre C, Passet V, Issenhuth-Jeanjean S, Tournebize R, Diancourt L, Grimont P (2009). Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS One 4:e4982
Sequence bin
- contigs
- 848
- total length
- 5,478,137 bp
- max length
- 41,972 bp
- mean length
- 6,461 bp
- N50
- 10,408
- L50
- 163
- N90
- 3,025
- L90
- 527
- N95
- 2,168
- L95
- 634
- %GC
- 57.33
- Ns
- 0
- gaps
- 0
- loci tagged
- 2,467
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 | 51 | 96 | |
scgMLST629_S | 629 | 552 | 87 |
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
- 4
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 2; ICEKp1 (incomplete)
- YbST
- 320-2LV
- CbST
- 0
- Aerobactin
- iuc 1
- AbST
- 17
- SmST
- 0
- RmpADC
- rmp 3; ICEKp1,-,-
- RmST
- 32,0,0
- wzi
- wzi1
- K_locus
- KL1
- K_type
- K1
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 99.99%
- K_locus_missing_genes
- KL1_06_wzc
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.13%
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- ybtS
- 8
- ybtQ
- 9
- ybtP
- 6
- ybtA
- 5
- irp2
- 13
- ybtU
- 6
- ybtT
- 7
- ybtE
- 7
- fyuA
- 6
- iucA
- 6
- iucB
- 1
- iucC
- 6
- iucD
- 1
- iutA
- 1
- iroN
- 1*-81%
- rmpA
- 11,-,-
- rmpD
- 5,-,2
- rmpC
- 6,2,-
- spurious_virulence_hits
- irp1_245*-59%;irp1_1*-0%;ybtX_96*-0%;iroN_16*-54%;iroB_6*-0%;iroD_1*-0%;rmpA_55*-0%;rmpA_88*-51%;rmpA_40*-45%
Analysis performed: 2023-07-21; Kleborate v2.3.2
Schemes and loci
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