Full information on isolate MEZ30_S7 (id:15857)
Projects
This isolate is a member of the following project:
- Ezzat_2021
- Klebsiella from South Africa
Provenance/primary metadata
- id
- 15857
- isolate
- MEZ30_S7
- sender
- Mohamed Ezzat, Zoonosis Science Center, University of Uppsala, Sweden
- curator
- Auto Tagger
- update history
- 12 updates show details
- date entered
- 2021-04-01
- datestamp
- 2023-01-22
- taxonomic designation
- K. pneumoniae
- isolation year
- 2018
- city
- KwaZulu-Natal
- country
- South Africa
- continent
- Africa
- source type
- Wild Animal
- host
- Wild Bird
- source lab
- Prof. Dr. Mohamed Ezzat El Zowalaty
- accession number
- PRJNA716986
Sequence bin
- contigs
- 165
- total length
- 5,504,273 bp
- max length
- 473,040 bp
- mean length
- 33,360 bp
- N50
- 155,451
- L50
- 13
- N90
- 32,588
- L90
- 42
- N95
- 17,619
- L95
- 53
- %GC
- 57.05
- Ns
- 99
- gaps
- 1
- loci tagged
- 704
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
- QC_warnings
- ambiguous_bases
- 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
- wzi5
- K_locus
- unknown (KL5)
- K_type
- unknown (K5)
- K_locus_problems
- ?-*
- K_locus_confidence
- None
- K_locus_identity
- 99.12%
- K_locus_missing_genes
- KL5_06_wzc,KL5_07,KL5_08_wzx,KL5_09,KL5_12,KL5_15_wcaJ,KL5_17_manC
- O_locus
- O3b
- O_type
- O3b
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 99.58%
- O_locus_missing_genes
- O3b_01_manC
- Tet_acquired
- tet(A).v1
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- spurious_resistance_hits
- fosA7*?-0%
Analysis performed: 2024-03-22; Kleborate v2.3.2
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 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 1106 (3 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1884 (3 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 1106 (3 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 1884 (3 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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