Full information on isolate ERR971951 (id:58972)
Projects
This isolate is a member of the following project:
- Musicha et al. 2019
- Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages (PMID: 30778540)
Provenance/primary metadata
- id
- 58972
- isolate
- ERR971951
- sender
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France
- curator
- Auto Tagger
- update history
- 2 updates show details
- date entered
- 2024-03-21
- datestamp
- 2024-03-21
- taxonomic designation
- K. pneumoniae
- isolation year
- 2013
- city
- Blantyre
- country
- Malawi
- continent
- Africa
- source type
- Human
- host
- Human
- source details
- CSF
- source lab
- Queen Elizabeth Central Hospital, Blantyre, Malawi
- comments
- Musicha 2019
- accession number
- ERR971951
Sequence bin
- contigs
- 106
- total length
- 5,583,049 bp
- max length
- 356,342 bp
- mean length
- 52,671 bp
- N50
- 131,326
- L50
- 15
- N90
- 53,386
- L90
- 40
- N95
- 26,212
- L95
- 48
- %GC
- 57.09
- Ns
- 88
- gaps
- 77
- loci tagged
- 693
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 | 627 | 99 | |
Analysis
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 1
- num_resistance_classes
- 9
- num_resistance_genes
- 16
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi50
- K_locus
- KL15
- K_type
- K15
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 99.76%
- O_locus
- O4
- O_type
- O4
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 99.66%
- AGly_acquired
- aac(6')-Ib-cr.v2;aadA*;aadA2
- Flq_acquired
- qnrS1
- Phe_acquired
- catII.2*;cmlA5
- Rif_acquired
- arr-2
- Sul_acquired
- sul1;sul2
- Tet_acquired
- tet(D)
- Tmt_acquired
- dfrA14.v2*
- Bla_acquired
- LAP-2;OXA-1;OXA-10;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-11.v1
- SHV_mutations
- 35Q
- Flq_mutations
- GyrA-83I;ParC-80I
- truncated_resistance_hits
- aac(3)-IIa.v1?-0%
Analysis performed: 2024-04-30; Kleborate v2.3.2
Schemes and loci
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Tools
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