Full information on isolate FMUL680 (id:22011)
Provenance/primary metadata
- id
- 22011
- isolate
- FMUL680
- sender
- Cátia Caneiras, Microbiology Research Laboratory in Environmental Health, Institute of Environmental Health, Faculty of Medicine, University of Lisbon, Portugal
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 8 updates show details
- date entered
- 2022-06-03
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2021
- city
- Lisbon
- country
- Portugal
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Purulent exudate
Sequence bin
- method
- Illumina
- contigs
- 88
- total length
- 5,581,723 bp
- max length
- 571,899 bp
- mean length
- 63,429 bp
- N50
- 351,014
- L50
- 7
- N90
- 45,309
- L90
- 22
- N95
- 21,014
- L95
- 30
- %GC
- 57.16
- Ns
- 1125
- gaps
- 17
- loci tagged
- 723
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 | 627 | 99 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2022-12-06
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 1
- resistance_score
- 2
- num_resistance_classes
- 4
- num_resistance_genes
- 3
- Yersiniabactin
- ybt 9; ICEKp3
- YbST
- 183-2LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi104
- K_locus
- KL51
- K_type
- K51
- K_locus_confidence
- High
- K_locus_identity
- 99.40%
- K_locus_missing_genes
- KL51_14_wcoZ
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.45%
- AGly_acquired
- aac(6')-Ib'.v1*
- Tmt_acquired
- dfrA14.v2*
- Bla_Carb_acquired
- KPC-3
- Flq_mutations
- GyrA-83I;ParC-80I
- truncated_resistance_hits
- SHV-187*?-82%
- ybtS
- 5
- ybtX
- 11
- ybtQ
- 6
- ybtP
- 5
- ybtA
- 1
- irp2
- 25
- irp1
- 318
- ybtU
- 9
- ybtT
- 5
- ybtE
- 123
- fyuA
- 11
Analysis performed: 2024-03-22; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_0_0_0_15_2_0_0
- Phylogroup
- Kp1
- Sublineage
- SL231
- Clonal group
- CG231
Similar isolates (determined by classification schemes)
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 | 48 (97 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (90 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 | 48 (97 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (90 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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