Full information on isolate 09-406B (id:2909)
Projects
Provenance/primary metadata
- id
- 2909
- isolate
- 09-406B
- sender
- Kat Holt, Melbourne U
- curator
- Auto Tagger
- update history
- 21 updates show details
- date entered
- 2015-06-01
- datestamp
- 2023-11-22
- taxonomic designation
- K. pneumoniae
- QC status
- 0100
- isolation year
- 2009
- country
- Vietnam
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Sputum
- infection
- Human_infection
- other source info
- Respiratory
- source lab
- Heiman Wertheim
- accession number
- ERS012013
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
- 1,376
- total length
- 5,662,361 bp
- max length
- 57,944 bp
- mean length
- 4,116 bp
- N50
- 14,062
- L50
- 122
- N90
- 2,261
- L90
- 510
- N95
- 1,194
- L95
- 675
- %GC
- 56.36
- Ns
- 206013
- gaps
- 2493
- loci tagged
- 1,633
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| Assembly size | ||
| Minimum N50 | N50 too low (warn threshold: 20,000) | |
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| MLST | 7 | 6 | 85 | |
| Ribosomal MLST | 53 | 53 | 100 | |
| scgMLST629_S | 629 | 409 | 65 | |
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
- 10
- num_resistance_genes
- 15
- Yersiniabactin
- ybt 15; ICEKp11 (incomplete)
- YbST
- 230-4LV
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi64
- K_locus
- unknown (KL64)
- K_type
- unknown (K64)
- K_locus_problems
- ?-
- K_locus_confidence
- None
- K_locus_identity
- 98.49%
- K_locus_missing_genes
- KL64_14_wcuK,KL64_18_manC,KL64_19_manB,KL64_20_rmlB
- O_locus
- O1/O2v1
- O_type
- O1
- O_locus_problems
- ?-
- O_locus_confidence
- Good
- O_locus_identity
- 98.62%
- O_locus_missing_genes
- O1/O2v1_03_wbbM
- 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
- Col_mutations
- PmrB-54%
- Flq_mutations
- GyrA-83I;GyrA-87Y;ParC-80I
- truncated_resistance_hits
- SHV-106*?-0%
- spurious_resistance_hits
- floR.v1*?-0%;floR.v2*?-0%;sul1?-63%
- ybtS
- 6
- ybtQ
- 22
- ybtP
- 4
- ybtA
- 39*
- ybtU
- 14
- ybtT
- 1
- ybtE
- 4
- fyuA
- 17
- spurious_virulence_hits
- irp2_220*-0%;ybtX_117*-0%
Analysis performed: 2024-02-13; Kleborate v2.3.2
Schemes and loci
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