Full information on isolate MVK-06F163 (id:12028)
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
- 12028
- isolate
- MVK-06F163
- sender
- Carla Rodrigues, Institut Pasteur, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 11 updates show details
- date entered
- 2020-02-12
- datestamp
- 2024-06-03
- 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
- 192
- total length
- 5,164,130 bp
- max length
- 232,352 bp
- mean length
- 26,897 bp
- N50
- 57,723
- L50
- 27
- N90
- 18,092
- L90
- 85
- N95
- 11,407
- L95
- 103
- %GC
- 57.61
- Ns
- 0
- gaps
- 0
- loci tagged
- 714
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
- 1
- resistance_score
- 0
- num_resistance_classes
- 0
- num_resistance_genes
- 0
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 393
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi21
- K_locus
- unknown (KL21)
- K_type
- unknown (K21)
- K_locus_problems
- ?-*
- K_locus_confidence
- None
- K_locus_identity
- 98.46%
- K_locus_missing_genes
- KL21_05_wzb,KL21_06_wzc,KL21_07_wcuD,KL21_08_wzy,KL21_09_wcuE,KL21_10_wcuC,KL21_11_wbaZ,KL21_12_wbaP,KL21_13_wcuA,KL21_14_wcaL,KL21_15_wzx
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_confidence
- High
- O_locus_identity
- 98.10%
- O_locus_missing_genes
- O1/O2v1_01_wzm
- Bla_chr
- SHV-1
- ybtS
- 81
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 243
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
Analysis performed: 2024-03-12; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_75_0_2_1_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL290
- Clonal group
- CG290
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 | 188 (46 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 271 (46 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 1498 (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 | 188 (46 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 271 (46 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 1498 (3 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 2500 (1 isolate) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 2966 (1 isolate) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 3577 (1 isolate) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 4094 (1 isolate) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 5014 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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