Full information on isolate ERR314522 (id:26996)
Projects
This isolate is a member of the following project:
- Ellington et al. 2019
- Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center (https://doi.org/10.1186/s13059-019-1785-1)
Provenance/primary metadata
- id
- 26996
- isolate
- ERR314522
- alias
- SAMEA2053941
- sender
- Sebastien Bridel, Institut Pasteur, Paris, France
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 7 updates show details
- date entered
- 2023-02-15
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 0
- city
- Unknown
- country
- UK
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Sequence bin
- method
- Unknown
- contigs
- 142
- total length
- 5,599,901 bp
- max length
- 507,950 bp
- mean length
- 39,436 bp
- N50
- 241,739
- L50
- 8
- N90
- 44,399
- L90
- 27
- N95
- 21,901
- L95
- 35
- %GC
- 57.06
- Ns
- 1382
- gaps
- 17
- loci tagged
- 689
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 | 626 | 99 | |
Analysis
rMLST species identification
| Rank | Taxon | Taxonomy | Support | Matches |
|---|---|---|---|---|
| SPECIES | Klebsiella pneumoniae | Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae | 100% |
Analysis performed: 2023-04-19
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 1
- num_resistance_classes
- 10
- num_resistance_genes
- 22
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi104
- K_locus
- KL51
- K_type
- K51
- K_locus_confidence
- High
- K_locus_identity
- 99.40%
- K_locus_missing_genes
- KL51_14_wcoZ
- O_locus
- O1/O2v2
- O_type
- O1
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.45%
- AGly_acquired
- aac(3)-IId^;aac(6')-Ib'.v1;aadA*;aadA2^;aph3-Ia.v1^;strA.v1;strB.v1
- Flq_acquired
- qnrS1
- MLS_acquired
- mphA
- Phe_acquired
- CatB4.v1?;catII.2*
- Sul_acquired
- sul1;sul2
- Tet_acquired
- tet(D)
- Tgc_acquired
- tmexC1*;tmexD1*;toprJ1*
- Tmt_acquired
- dfrA12
- Bla_acquired
- OXA-1;OXA-9.v1?;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-79%
- Flq_mutations
- GyrA-83I;ParC-80I
Analysis performed: 2024-03-27; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_88_0_0_11_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL231
- Clonal group
- CG231
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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Analysis: