Full information on isolate NMI2273_16 (id:7106)
Projects
Provenance/primary metadata
- id
- 7106
- isolate
- NMI2273_16
- sender
- Radek Izdebski, National Medecines Institute Chelmska 30/34 00-725 Warsaw, Poland
- curator
- Audrey Combary, Institut Pasteur, Paris, France (E-mail: audrey.combary@pasteur.fr)
- update history
- 19 updates show details
- date entered
- 2018-03-23
- datestamp
- 2026-02-12
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0000
- isolation year
- 2016
- city
- Torun
- country
- Poland
- continent
- Europe
- host
- human
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
- method
- Illumina
- contigs
- 66
- total length
- 5,688,618 bp
- max length
- 1,051,407 bp
- mean length
- 86,192 bp
- N50
- 369,355
- L50
- 6
- N90
- 99,497
- L90
- 18
- N95
- 56,453
- L95
- 21
- %GC
- 56.94
- Ns
- 0
- gaps
- 0
- loci tagged
- 4,307
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 | |
| SL147_cgMLST | 852 | 851 | 99 | |
| SL307_cgMLST | 947 | 658 | 69 | |
| Kpn_cgMLST | 2752 | 2745 | 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
- 5
- num_resistance_genes
- 7
- 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
- Very high
- K_locus_identity
- 100.00%
- O_locus
- O1/O2v1
- O_type
- O2a
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.64%
- AGly_acquired
- aac(3)-IId^;aac(6')-Ib3^;aph(3')-VI;rmtC
- Sul_acquired
- sul1
- Bla_acquired
- CMY-6
- 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: 2025-05-14; Kleborate v2.3.2
Similar isolates (determined by LIN codes)
- Scheme
- scgMLST629_S
- LIN code
- 0_0_197_0_4_27_0_0_0_0
- Phylogroup
- Kp1
- Sublineage
- SL147
- Clonal group
- CG147
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_197_0_4_27 | 7 | 1 |
| 0_0_197_0_4_27_0 | 4 | 1 |
| 0_0_197_0_4_27_0_0 | 2 | 1 |
| 0_0_197_0_4_27_0_0_0 | 1 | 1 |
| 0_0_197_0_4_27_0_0_0_0 | 0 | 1 |
| 0 | 610 | 41312 |
| 0_0 | 585 | 41312 |
| 0_0_197 | 190 | 2451 |
| 0_0_197_0 | 43 | 2414 |
| 0_0_197_0_4 | 10 | 1593 |
| 0_0_197_0_4_27 | 7 | 1 |
| 0_0_197_0_4_27_0 | 4 | 1 |
| 0_0_197_0_4_27_0_0 | 2 | 1 |
| 0_0_197_0_4_27_0_0_0 | 1 | 1 |
| 0_0_197_0_4_27_0_0_0_0 | 0 | 1 |
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 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 50 (758 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 51 (750 isolates) |
| klebs_species_v1.0 | scgMLST629_S | Single-linkage | 610 | experimental | 1 (16003 isolates) |
| klebs_subspecies_v1.0 | scgMLST629_S | Single-linkage | 585 | experimental | 1 (15951 isolates) |
| klebs_sublineage_v1.0 | scgMLST629_S | Single-linkage | 190 | experimental | 50 (758 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 51 (750 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: