Full information on isolate UI_3324 (id:3150)
Projects
Provenance/primary metadata
- id
- 3150
- isolate
- UI_3324
- sender
- Kat Holt, Melbourne U
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 27 updates show details
- date entered
- 2015-06-01
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2003
- country
- Laos
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Blood
- infection
- Human_invasive
- other source info
- sterile
- source lab
- David Dance
- accession number
- ERS011886
Publication (1)
- Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J, Brisse S, Cao H, Wilksch J, Gorrie C, Schultz MB, Edwards DJ, Nguyen KV, Nguyen TV, Dao TT, Mensink M, Minh VL, Nhu NT, Schultsz C, Kuntaman K, Newton PN, Moore CE, Strugnell RA, Thomson NR (2015). Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A 112:E3574-81
Sequence bin
- contigs
- 139
- total length
- 5,434,658 bp
- max length
- 386,041 bp
- mean length
- 39,099 bp
- N50
- 250,239
- L50
- 9
- N90
- 49,946
- L90
- 26
- N95
- 18,910
- L95
- 36
- %GC
- 56.94
- Ns
- 3052
- gaps
- 51
- loci tagged
- 3,940
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
- 1
- num_resistance_classes
- 7
- num_resistance_genes
- 11
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi325
- K_locus
- KL114
- K_type
- unknown (KL114)
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.55%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.54%
- AGly_acquired
- aac(3)-IIa.v1;aac(6')-Iaf*;ant(2'')-Ia;aph3-Ia.v1*?
- MLS_acquired
- mphA
- Phe_acquired
- cmlA6
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- SCO-1;TEM-1D.v1^
- Bla_ESBL_acquired
- SHV-2A^
- SHV_mutations
- 238S;35Q
- spurious_resistance_hits
- aadA8b?-74%;aadA?-74%
Analysis performed: 2024-02-20; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_2_0_1_0_0_0_0
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 (13578 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13526 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (88 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13578 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13526 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (88 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 2724 (1 isolate) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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