Full information on isolate ST258-490 (id:1681)
Projects
Provenance/primary metadata
- id
- 1681
- isolate
- ST258-490
- sender
- Suzanne Bialek, AP-HP
- curator
- Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
- update history
- 85 updates show details
- date entered
- 2013-07-01
- datestamp
- 2022-11-03
- taxonomic designation
- K. pneumoniae
- phylogroup from ST
- Kp1 (7 loci)
- QC status
- 0100
- isolation year
- 2006
- city
- Tel Aviv
- country
- Israel
- continent
- Asia
- source type
- Human
- host
- Human
- source details
- Urine
- resistance info
- KPC
- comments
- Chmelnitsky et al. J. Bacteriol. 2012
- accession number
- ALIS01
Publications (3)
- Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S (2014). Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 20:1812-20
- Chmelnitsky I, Doniger T, Shklyar M, Naparstek L, Banin E, Edgar R, Carmeli Y (2012). Draft genome sequence of an extremely drug-resistant KPC-producing Klebsiella pneumoniae ST258 epidemic strain. J Bacteriol 194:6014
- Onori R, Gaiarsa S, Comandatore F, Pongolini S, Brisse S, Colombo A, Cassani G, Marone P, Grossi P, Minoja G, Bandi C, Sassera D, Toniolo A (2015). Tracking Nosocomial Klebsiella pneumoniae Infections and Outbreaks by Whole-Genome Analysis: Small-Scale Italian Scenario within a Single Hospital. J Clin Microbiol 53:2861-8
Sequence bin
- contigs
- 569
- total length
- 5,707,592 bp
- max length
- 168,073 bp
- mean length
- 10,031 bp
- N50
- 59,798
- L50
- 31
- N90
- 11,738
- L90
- 107
- N95
- 3,699
- L95
- 147
- %GC
- 56.90
- Ns
- 11
- gaps
- 11
- loci tagged
- 5,396
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | too many contigs (fail threshold: 501) | |
| 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
- QC_warnings
- ambiguous_bases
- virulence_score
- 0
- resistance_score
- 2
- num_resistance_classes
- 7
- num_resistance_genes
- 8
- YbST
- 0
- CbST
- 0
- AbST
- 0
- SmST
- 0
- RmST
- 0
- wzi
- wzi154
- K_locus
- KL107
- K_type
- unknown (KL107)
- K_locus_problems
- none
- K_locus_confidence
- Very high
- K_locus_identity
- 100.00%
- O_locus
- O1/O2v2
- O_type
- O2afg
- O_locus_problems
- none
- O_locus_confidence
- Very high
- O_locus_identity
- 98.38%
- AGly_acquired
- aac(6')-Ib'.v1;aadA2^;aph3-Ia.v1^
- MLS_acquired
- mphA
- Phe_acquired
- catA1^
- Sul_acquired
- sul1
- Tmt_acquired
- dfrA12
- Bla_Carb_acquired
- KPC-3
- Bla_chr
- SHV-11.v1
- SHV_mutations
- 35Q
- Omp_mutations
- OmpK35-25%;OmpK36GD
- Flq_mutations
- GyrA-83I;ParC-80I
- truncated_resistance_hits
- OXA-9.v1*-42%;TEM-122*?-83%
Analysis performed: 2024-02-09; 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 | 57 (3460 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 61 (3217 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 80 (1591 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 82 (1565 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 104 (1455 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 837 (36 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 954 (23 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4080 (2 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 | 57 (3460 isolates) |
| klebs_clonalgroup_v1.0 | scgMLST629_S | Single-linkage | 43 | experimental | 61 (3217 isolates) |
| klebs_threshold10_v1.0 | scgMLST629_S | Single-linkage | 10 | experimental | 80 (1591 isolates) |
| klebs_threshold7_v1.0 | scgMLST629_S | Single-linkage | 7 | experimental | 82 (1565 isolates) |
| klebs_threshold4_v1.0 | scgMLST629_S | Single-linkage | 4 | experimental | 104 (1455 isolates) |
| klebs_threshold2_v1.0 | scgMLST629_S | Single-linkage | 2 | experimental | 837 (36 isolates) |
| klebs_threshold1_v1.0 | scgMLST629_S | Single-linkage | 1 | experimental | 954 (23 isolates) |
| klebs_threshold0_v1.0 | scgMLST629_S | Single-linkage | 0 | experimental | 4080 (2 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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