Full information on isolate M6 (id:8694)
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
- 8694
- isolate
- M6
- 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
- 661 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
- 137
- total length
- 5,513,561 bp
- max length
- 296,528 bp
- mean length
- 40,245 bp
- N50
- 141,749
- L50
- 14
- N90
- 30,062
- L90
- 47
- N95
- 15,691
- L95
- 60
- %GC
- 57.23
- Ns
- 0
- gaps
- 0
- loci tagged
- 718
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
- 11
- num_resistance_genes
- 16
- Yersiniabactin
- ybt 14; ICEKp5
- YbST
- 376-1LV
- 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
- 85.78%
- K_locus_missing_genes
- KL107_05_wzb,KL107_06_wzc,KL107_07_wbaP,KL107_08,KL107_09,KL107_10,KL107_12,KL107_13,KL107_14,KL107_15
- O_locus
- unknown (O1/O2v2)
- O_type
- unknown (O1)
- O_locus_confidence
- None
- O_locus_identity
- 98.38%
- O_locus_missing_genes
- O1/O2v2_01_wzm,O1/O2v2_02_wzt,O1/O2v2_03_wbbM,O1/O2v2_04_glf,O1/O2v2_05_wbbN,O1/O2v2_06_wbbO
- AGly_acquired
- aac(6')-Ib;aadA2^;rmtF
- Flq_acquired
- qepA2*;qnrB4
- MLS_acquired
- mphA?
- Phe_acquired
- catA1^
- Rif_acquired
- arr-2
- Sul_acquired
- sul1
- Tet_acquired
- tet(B).v2*;tetR
- Tmt_acquired
- dfrA12
- Bla_acquired
- DHA-1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_Carb_acquired
- OXA-232
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- Omp_mutations
- OmpK35-30%;OmpK36TD
- Flq_mutations
- GyrA-83I;GyrA-87G;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_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 50 (69 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 127 (66 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 141 (42 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 154 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 165 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 190 (2 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) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 50 (69 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 127 (66 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 141 (42 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 154 (2 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 165 (2 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 190 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
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