Full information on isolate NMI1183_20 (id:14524)
Projects
Provenance/primary metadata
- id
- 14524
- isolate
- NMI1183_20
- sender
- Radek Izdebski, National Medecines Institute Chelmska 30/34 00-725 Warsaw, Poland
- curator
- Auto Tagger
- update history
- 12 updates show details
- date entered
- 2020-08-07
- datestamp
- 2023-01-22
- taxonomic designation
- K. pneumoniae
- QC status
- 0000
- isolation year
- 2020
- city
- Warsaw
- country
- Poland
- continent
- Europe
- source type
- Human
- host
- Human
- source details
- Unknown
Publication (1)
- Biedrzycka M, Urbanowicz P, Guzek A, Brisse S, Gniadkowski M, Izdebski R (2021). Dissemination of Klebsiella pneumoniae ST147 NDM-1 in Poland, 2015-19. J Antimicrob Chemother 76:2538-2545
Sequence bin
- contigs
- 88
- total length
- 5,873,301 bp
- max length
- 941,786 bp
- mean length
- 66,743 bp
- N50
- 311,559
- L50
- 6
- N90
- 91,902
- L90
- 19
- N95
- 76,112
- L95
- 22
- %GC
- 56.64
- Ns
- 0
- gaps
- 0
- loci tagged
- 721
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 | 628 | 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
- 8
- num_resistance_genes
- 13
- Yersiniabactin
- ybt 16; ICEKp12
- YbST
- 280
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi64
- K_locus
- KL64
- K_type
- K64
- K_locus_problems
- none
- K_locus_confidence
- Perfect
- K_locus_identity
- 100.00%
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- ?
- O_locus_confidence
- Good
- O_locus_identity
- 98.64%
- AGly_acquired
- aac(3)-IIa.v1^;aac(6')-Ib-cr.v2;strA.v1;strB.v1
- Flq_acquired
- qnrB1.v1
- Phe_acquired
- CatB4.v1;catA1^
- Sul_acquired
- sul1
- Tet_acquired
- tet(A).v1
- Tmt_acquired
- dfrA1.v1
- Bla_acquired
- OXA-1;TEM-1D.v1^
- Bla_Carb_acquired
- NDM-1
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- Omp_mutations
- OmpK35-7%
- Flq_mutations
- GyrA-83I;ParC-80I
- ybtS
- 6
- ybtX
- 15
- ybtQ
- 5
- ybtP
- 4
- ybtA
- 11
- irp2
- 125
- irp1
- 129
- ybtU
- 2
- ybtT
- 11
- ybtE
- 51
- fyuA
- 2
Analysis performed: 2024-03-13; 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 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 50 (740 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 51 (733 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 77 (357 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 79 (351 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 82 (179 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 208 (29 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 1760 (5 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 2142 (5 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (13436 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (13415 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 50 (740 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 51 (733 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 77 (357 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 79 (351 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 82 (179 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 208 (29 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 1760 (5 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 2142 (5 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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