Full information on isolate MVK-06F119 (id:12009)
Projects
This isolate is a member of the following project:
- Rodrigues et al 2022_MSpectrum
- Collection of KpSC genomes studied in 'High prevalence of Klebsiella pneumoniae in EU food as determined using culture and molecular detection methods' (PMID: 35196810)
Provenance/primary metadata
- id
- 12009
- isolate
- MVK-06F119
- sender
- Carla Rodrigues, Institut Pasteur, France
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 9 updates show details
- date entered
- 2020-02-12
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2019
- country
- Denmark
- continent
- Europe
- host
- environment
- source details
- chicken meat
- source lab
- SSI
Publication (1)
- Rodrigues C, Hauser K, Cahill N, Ligowska-Marzęta M, Centorotola G, Cornacchia A, Garcia Fierro R, Haenni M, Nielsen EM, Piveteau P, Barbier E, Morris D, Pomilio F, Brisse S (2022). High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods. Microbiol Spectr 10:e0237621
Sequence bin
- method
- Unknown
- contigs
- 177
- total length
- 5,163,084 bp
- max length
- 218,128 bp
- mean length
- 29,170 bp
- N50
- 70,217
- L50
- 23
- N90
- 21,869
- L90
- 75
- N95
- 12,586
- L95
- 91
- %GC
- 57.61
- Ns
- 0
- gaps
- 0
- loci tagged
- 699
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 | 626 | 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
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 1
- num_resistance_genes
- 1
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi243
- K_locus
- unknown (KL13)
- K_type
- unknown (K13)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 98.94%
- K_locus_missing_genes
- KL13_06_wzc,KL13_07_wcuD,KL13_08_wclX,KL13_09_wzy,KL13_10_wcuF,KL13_11_wzx,KL13_12_wcuL,KL13_13_wcoW,KL13_14,KL13_17_manC,KL13_18_manB
- O_locus
- unknown (O5)
- O_type
- unknown (O5)
- O_locus_problems
- ?-*
- O_locus_confidence
- Low
- O_locus_identity
- 93.85%
- O_locus_missing_genes
- O5_01_manC,O5_02_manB
- Fcyn_acquired
- fosA7*
- Bla_chr
- SHV-208*
- SHV_mutations
- 35Q
Analysis performed: 2024-03-12; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_450_0_0_0_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL10067
- Clonal group
- CG10333
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
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 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 765 (3 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1251 (2 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 765 (3 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1251 (2 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 2222 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 2486 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2950 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3560 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 4077 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4996 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: