Full information on isolate KpO3210 (id:1551)
Projects
Provenance/primary metadata
- id
- 1551
- isolate
- KpO3210
- sender
- Suzanne Bialek, AP-HP
- curator
- Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
- update history
- 676 updates show details
- date entered
- 2013-04-11
- datestamp
- 2025-07-18
- taxonomic designation
- K. pneumoniae
- QC status
- 0100
- isolation year
- 2010
- city
- Madrid
- country
- Spain
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Blood
- resistance info
- OXA-1, OXA-48, TEM-1, SHV-76, CTX-M-15
- comments
- >6000 contigs; ST405
- accession number
- AMRH01
Publication (1)
- Wesselink JJ, López-Camacho E, de la Peña S, Ramos-Ruiz R, Ruiz-Carrascoso G, Lusa-Bernal S, Fernández-Soria VM, Gómez-Gil R, Gomez-Puertas P, Mingorance J (2012). Genome sequence of OXA-48 carbapenemase-producing Klebsiella pneumoniae KpO3210. J Bacteriol 194:6981
Sequence bin
- method
- Illumina
- contigs
- 6,704
- total length
- 5,147,256 bp
- max length
- 4,926 bp
- mean length
- 768 bp
- N50
- 1,002
- L50
- 1,603
- N90
- 372
- L90
- 4,863
- N95
- 289
- L95
- 5,648
- %GC
- 56.89
- Ns
- 0
- gaps
- 0
- loci tagged
- 1,278
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| Assembly size | ||
| Minimum N50 | N50 too low (fail threshold: 10,000) | |
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| MLST | 7 | 3 | 42 | |
| Ribosomal MLST | 53 | 25 | 47 | |
| scgMLST629_S | 629 | 233 | 37 | |
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
- N50
- virulence_score
- 0
- resistance_score
- 0
- num_resistance_classes
- 3
- num_resistance_genes
- 2
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- K_locus
- unknown (KL151)
- K_type
- unknown (KL151)
- K_locus_problems
- ?-+
- K_locus_confidence
- None
- K_locus_identity
- 96.94%
- K_locus_missing_genes
- KL151_01_galF,KL151_03_wzi,KL151_04_wza,KL151_07,KL151_09,KL151_11_wzy,KL151_12,KL151_13_wfgD,KL151_14,KL151_15,KL151_16_gnd,KL151_17_rmlB,KL151_18_rmlA,KL151_21_ugd
- O_locus
- unknown (O4)
- O_type
- unknown (O4)
- O_locus_problems
- ?-
- O_locus_confidence
- None
- O_locus_identity
- 99.69%
- O_locus_missing_genes
- O4_01_hydrolase,O4_02_hypothetical,O4_03_hypothetical,O4_04_wzt
- AGly_acquired
- strA.v1^
- Tmt_acquired
- dfrA14.v2*
- Bla_chr
- SHV-76
- SHV_mutations
- 35Q
- Omp_mutations
- OmpK35-25%;OmpK36-21%
- Col_mutations
- MgrB-51%;PmrB-45%
- truncated_resistance_hits
- CatB4.v1?-90%;aac(3)-IIa.v1?-0%;aac(6')-Ib-cr.v2?-90%;aph(6)-Id.v2?-88%;qnrB1.v1*?-20%
- spurious_resistance_hits
- CTX-M-103?-77%;OXA-1?-0%;OXA-48?-0%;TEM-117?-0%;fosA7*?-0%;sul2?-0%
- ybtP
- 128*-0%
- ybtE
- 69*-89%
- spurious_virulence_hits
- ybtQ_88*-0%;ybtU_13*-0%;ybtX_1*-49%;ybtA_71*-0%;ybtT_42*-57%;ybtS_93*-0%;ybtA_39*-43%;ybtT_39*-0%
Analysis performed: 2025-03-14; Kleborate v2.3.2
Schemes and loci
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