Full information on isolate NMI6860/12 (id:22907)
Projects
This isolate is a member of the following project:
- Public isolates
- This project contains the isolates that should be publicly available through the public access database.
Provenance/primary metadata
- id
- 22907
- isolate
- NMI6860/12
- sender
- Radek Izdebski, National Medecines Institute Chelmska 30/34 00-725 Warsaw, Poland
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 5 updates show details
- date entered
- 2023-01-16
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- isolation year
- 2012
- city
- Lublin
- country
- Poland
- continent
- Europe
- source type
- Human
- host
- human
- source details
- rectal swab
Sequence bin
- contigs
- 140
- total length
- 5,456,185 bp
- max length
- 407,676 bp
- mean length
- 38,973 bp
- N50
- 129,977
- L50
- 12
- N90
- 57,415
- L90
- 35
- N95
- 34,410
- L95
- 42
- %GC
- 57.17
- Ns
- 0
- gaps
- 0
- loci tagged
- 690
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 | 52 | 98 | |
| scgMLST629_S | 629 | 628 | 99 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2023-01-17
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- virulence_score
- 0
- resistance_score
- 2
- num_resistance_classes
- 6
- num_resistance_genes
- 6
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi7
- K_locus
- KL7
- K_type
- K7
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 98.54%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.59%
- AGly_acquired
- aadA1.v1^
- Sul_acquired
- sul1
- Tet_acquired
- tet(A).v1
- Tmt_acquired
- dfrA1.v2
- Bla_ESBL_acquired
- SHV-5
- Bla_Carb_acquired
- VIM-4?
- SHV_mutations
- 238S;240K
- truncated_resistance_hits
- aac(6')-Ib7*-28%
Analysis performed: 2024-03-22; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_127_2_1_0_0_2_0_0
Schemes and loci
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Tools
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