Full information on isolate 09-0079m (id:2898)
Projects
Provenance/primary metadata
- id
- 2898
- isolate
- 09-0079m
- sender
- Kat Holt, Melbourne U
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 30 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
- 2009
- country
- Vietnam
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Blood
- infection
- Human_invasive
- other source info
- sterile
- source lab
- Heiman Wertheim
- accession number
- ERS011798
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
- 324
- total length
- 5,856,270 bp
- max length
- 478,556 bp
- mean length
- 18,075 bp
- N50
- 182,523
- L50
- 11
- N90
- 26,454
- L90
- 42
- N95
- 12,836
- L95
- 57
- %GC
- 56.75
- Ns
- 16689
- gaps
- 228
- loci tagged
- 3,898
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 | 52 | 98 | |
| scgMLST629_S | 629 | 616 | 97 | |
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
- 1
- resistance_score
- 1
- num_resistance_classes
- 9
- num_resistance_genes
- 15
- Yersiniabactin
- ybt 15; ICEKp11
- YbST
- 230
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi64
- K_locus
- KL64
- K_type
- K64
- K_locus_problems
- none
- K_locus_confidence
- Perfect
- K_locus_identity
- 100.00%
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.64%
- AGly_acquired
- aadA*;ant(2'')-Ia;rmtB;strA.v1^;strB.v1
- Phe_acquired
- cmlA5
- Rif_acquired
- arr-2
- Sul_acquired
- sul2
- Tet_acquired
- tet(A).v2;tet(G).v1
- Tmt_acquired
- dfrA23
- Bla_acquired
- OXA-10;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15;VEB-1
- Bla_chr
- SHV-1^
- Flq_mutations
- GyrA-83I;GyrA-87Y;ParC-80I
- spurious_resistance_hits
- floR.v1*?-0%;floR.v2*?-0%;sul1?-63%
- ybtS
- 6
- ybtX
- 15
- ybtQ
- 22
- ybtP
- 4
- ybtA
- 1
- irp2
- 37
- irp1
- 34
- ybtU
- 14
- ybtT
- 1
- ybtE
- 4
- fyuA
- 17
Analysis performed: 2024-02-13; 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 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (88 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (82 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (88 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (82 isolates) |
Schemes and loci
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Tools
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