Full information on isolate M2 (id:8693)
Projects
This isolate is a member of the following project:
- Public isolates
- This project contains the isolates that should be publicly available through the public access database.
Provenance/primary metadata
- id
- 8693
- isolate
- M2
- sender
- siddhi Desai, Dr. Devarshi Gajjar's lab (DGL), Deaprtment of Microbiology and Biotechnology centre, Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India,
- curator
- Martin Rethoret-Pasty, Institut Pasteur, Paris, France (E-mail: martin.rethoret-pasty@pasteur.fr)
- update history
- 672 updates show details
- date entered
- 2019-05-21
- datestamp
- 2024-06-03
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2016
- city
- Surat
- country
- India
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Urine
- infection
- UTI
- resistance info
- MDR
Sequence bin
- contigs
- 99
- total length
- 5,398,260 bp
- max length
- 330,500 bp
- mean length
- 54,528 bp
- N50
- 182,522
- L50
- 11
- N90
- 38,076
- L90
- 36
- N95
- 22,931
- L95
- 44
- %GC
- 57.36
- Ns
- 0
- gaps
- 0
- loci tagged
- 717
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
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
- 1
- resistance_score
- 2
- num_resistance_classes
- 10
- num_resistance_genes
- 12
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 376
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi104
- K_locus
- unknown (KL107)
- K_type
- unknown (KL107)
- K_locus_problems
- ?-+
- K_locus_confidence
- None
- K_locus_identity
- 83.29%
- K_locus_missing_genes
- KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_11_gnd,KL107_12,KL107_13,KL107_14,KL107_15,KL107_16_ugd
- O_locus
- unknown (OL102)
- O_type
- unknown (OL102)
- O_locus_confidence
- None
- O_locus_identity
- 74.03%
- O_locus_missing_genes
- OL102_01_rfbB,OL102_02_rfbA,OL102_03_rfbD,OL102_04_rfbC,OL102_05_wbbL,OL102_06_rhamnan,OL102_07_wzm,OL102_08_wzt
- AGly_acquired
- aac(6')-Ib;aadA2^;rmtF
- Flq_acquired
- qnrS1
- MLS_acquired
- mphA
- Phe_acquired
- catA1^
- Rif_acquired
- arr-2
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA12
- Bla_acquired
- TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_Carb_acquired
- OXA-232
- Bla_chr
- SHV-1^
- Omp_mutations
- OmpK35-30%;OmpK36TD
- Flq_mutations
- GyrA-83I;ParC-80I
- ybtS
- 4
- ybtX
- 4
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 1
- irp2
- 8
- irp1
- 8
- ybtU
- 2
- ybtT
- 4
- ybtE
- 4
- fyuA
- 2
Analysis performed: 2024-03-12; Kleborate v2.3.2
Similar isolates (determined by classification schemes)
Experimental schemes are subject to change and are not a stable part of the nomenclature.
| Classification scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
|---|---|---|---|---|---|
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (88 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (82 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13437 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13416 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 48 (88 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 49 (82 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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