Full information on isolate EGD-HP19 (id:1712)
Projects
Provenance/primary metadata
- id
- 1712
- isolate
- EGD-HP19
- sender
- Suzanne Bialek, AP-HP
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 48 updates show details
- date entered
- 2013-08-27
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0100
- isolation year
- 2010
- country
- India
- continent
- Asia
- source type
- Environment
- host
- Environment
- source details
- Nitro-aromatics containing industrial waste water
- source lab
- Environmental Genomics Division, CSIR-NEERI, India
- comments
- Apparently contaminated with some contigs from Pantoea, implying detection of double rMLST alleles at some rMLST loci - corrected
- accession number
- AUTW01
Publication (1)
- Pal RR, Khardenavis AA, Purohit HJ (2015). Identification and monitoring of nitrification and denitrification genes in Klebsiella pneumoniae EGD-HP19-C for its ability to perform heterotrophic nitrification and aerobic denitrification. Funct Integr Genomics 15:63-76
Sequence bin
- contigs
- 904
- total length
- 6,080,708 bp
- max length
- 211,533 bp
- mean length
- 6,727 bp
- N50
- 74,585
- L50
- 24
- N90
- 2,972
- L90
- 128
- N95
- 727
- L95
- 396
- %GC
- 56.84
- Ns
- 0
- gaps
- 0
- loci tagged
- 3,923
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| 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
- virulence_score
- 0
- resistance_score
- 1
- num_resistance_classes
- 7
- num_resistance_genes
- 6
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi178
- K_locus
- KL166
- K_type
- unknown (KL166)
- K_locus_problems
- ?-
- K_locus_confidence
- Good
- K_locus_identity
- 99.14%
- K_locus_missing_genes
- KL166_02_cpsACP,KL166_13_wcuC
- O_locus
- O3b
- O_type
- O3b
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.27%
- AGly_acquired
- aadA*
- Flq_acquired
- qnrA1
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA5
- Bla_acquired
- OXA-9.v1
- Bla_ESBL_acquired
- SHV-12
- SHV_mutations
- 238S;240K;35Q
- Col_mutations
- PmrB-40%
- truncated_resistance_hits
- TEM-150*?-0%;aac(6')-Ib'.v1*?-0%;cmlA5*?-0%;ereA2?-0%
Analysis performed: 2024-02-09; Kleborate v2.3.2
Schemes and loci
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