Full information on isolate NMI650_19 (id:14499)
Projects
Provenance/primary metadata
- id
- 14499
- isolate
- NMI650_19
- 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
- 14 updates show details
- date entered
- 2020-08-07
- datestamp
- 2026-02-12
- taxonomic designation
- K. pneumoniae
- QC status
- x121
- isolation year
- 2019
- 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
- method
- Illumina
- contigs
- 3,927
- total length
- 7,401,865 bp
- max length
- 607,865 bp
- mean length
- 1,885 bp
- N50
- 208,194
- L50
- 12
- N90
- 399
- L90
- 1,662
- N95
- 328
- L95
- 2,690
- %GC
- 56.14
- Ns
- 0
- gaps
- 0
- loci tagged
- 702
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| Assembly size | assembly size too large (fail threshold: 6,132,847) | |
| Minimum N50 | ||
| %GC | %GC too low (fail threshold: 56.351) |
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 | 621 | 98 | |
Analysis
rMLST species identification
Analysis performed: 2022-11-02
Kleborate
- species
- Klebsiella pneumoniae
- species_match
- strong
- QC_warnings
- total_size
- virulence_score
- 1
- resistance_score
- 2
- num_resistance_classes
- 9
- num_resistance_genes
- 15
- 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
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.62%
- AGly_acquired
- aac(3)-IIa.v1^;aac(6')-Ib-cr.v2;aadA5;strA.v1;strB.v1
- Flq_acquired
- qnrB1.v1
- Phe_acquired
- CatB4.v1
- Sul_acquired
- sul1
- Tet_acquired
- tet(A).v1
- Tmt_acquired
- dfrA1.v1;dfrA17
- Bla_acquired
- OXA-1;TEM-1D.v1^
- Bla_ESBL_acquired
- CTX-M-15
- Bla_Carb_acquired
- NDM-1
- Bla_chr
- SHV-11.v1^
- SHV_mutations
- 35Q
- Omp_mutations
- OmpK35-7%
- Flq_mutations
- GyrA-83I;ParC-80I
- truncated_resistance_hits
- qnrB5*?-84%
- 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
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Third party:
Analysis: