Full information on isolate MVK-06F135 (id:12033)
Projects
Provenance/primary metadata
- id
- 12033
- isolate
- MVK-06F135
- sender
- Carla Rodrigues
- curator
- Carla Rodrigues, Institut Pasteur, France (E-mail: carla.parada-rodrigues@pasteur.fr)
- update history
- 11 updates show details
- date entered
- 2020-02-12
- datestamp
- 2024-09-24
- taxonomic designation
- K. variicola subsp. variicola
- QC status
- 0000
- isolation year
- 2019
- country
- France, Italy, Spain
- host
- environment
- source details
- salad
- source lab
- SSI
- accession number
- ERS8941038
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
- 239
- total length
- 5,683,275 bp
- max length
- 262,142 bp
- mean length
- 23,780 bp
- N50
- 45,542
- L50
- 36
- N90
- 15,905
- L90
- 113
- N95
- 7,690
- L95
- 138
- %GC
- 57.43
- Ns
- 0
- gaps
- 0
- loci tagged
- 683
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 | 610 | 96 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella variicola | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella variicola | 100% |
Analysis performed: 2022-11-02
Kleborate
- species
- Klebsiella variicola subsp. variicola
- 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
- wzi159
- K_locus
- unknown (KL30)
- K_type
- unknown (K30)
- K_locus_problems
- ?-+*
- K_locus_confidence
- None
- K_locus_identity
- 94.52%
- K_locus_missing_genes
- KL30_06_wzc,KL30_07_wcuL,KL30_08_wzx,KL30_09_wcuD,KL30_10_wzy,KL30_12_wckO,KL30_13_wckN,KL30_14,KL30_15_wcuG,KL30_16_wcaJ,KL30_18_manC,KL30_19_manB
- O_locus
- O3/O3a
- O_type
- O3/O3a
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.73%
- O_locus_missing_genes
- O3/O3a_01_manC,O3/O3a_02_manB
- Bla_chr
- LEN-22*
- Omp_mutations
- OmpK35-0%
Analysis performed: 2025-05-14; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 1_0_126_0_1_0_0_0_0_0
- Phylogroup
- Kp3
- Sublineage
- SL146
- Clonal group
- CG146
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 | 12 (4 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 12 (3 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 | 12 (4 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 12 (3 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 2237 (1 isolate) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 2502 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2969 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3580 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 4097 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 5017 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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