Full information on isolate KpMDU1 (id:1677)

Projects

This isolate is a member of the following projects:

Public isolates: This project contains the isolates that should be publicly available through the public access database.
published_genomes: All isolates with published genome imported in BIGSdb, and validated for scgMLST_S study
Bialek et al 2014_EID: 167 isolates from Bialek et al. in which the scgMLST-634 scheme was defined (PMID: 25341126)
Isolates Excluded (failed QC): KlebNET-GSP qc

id: 1677
isolate: KpMDU1
sender: Suzanne Bialek, AP-HP
curator: Sebastien Bridel, Institut Pasteur, Paris, France (E-mail: sbridel@pasteur.fr)
update history: 92 updates show details
date entered: 2013-06-21
datestamp: 2022-11-03
taxonomic designation: K. pneumoniae
phylogroup from ST: Kp1 (7 loci)
QC status: 0100
isolation year: 2012
country: Australia
continent: Oceania
source type: Human
host: Human
source details: Unknown
resistance info: KPC-2
comments: Direct submission
accession number: AMWO01

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
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

Check	Status	Warn/fail reason
Number of contigs		too many contigs (fail threshold: 501)
Assembly size
Minimum N50		N50 too low (warn threshold: 20,000)
%GC

Scheme	Scheme loci	Designated loci	Annotation
Scheme	Scheme loci	Designated loci	Score	Status
MLST	7	7	100
Ribosomal MLST	53	52	98
scgMLST629_S	629	564	89

Rank	Taxon	Taxonomy	Support	Matches
SPECIES	Klebsiella pneumoniae	Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae	100%

Analysis performed: 2022-11-02

species: Klebsiella pneumoniae
species_match: strong
QC_warnings: ambiguous_bases
virulence_score: 1
resistance_score: 2
num_resistance_classes: 8
num_resistance_genes: 8
Yersiniabactin: ybt 13; ICEKp2 (truncated)
YbST: 301
CbST: 0
AbST: 0
SmST: 0
RmST: 0
wzi: wzi29
K_locus: unknown (KL106)
K_type: unknown (KL106)
K_locus_problems: ?-
K_locus_confidence: None
K_locus_identity: 99.90%
K_locus_missing_genes: KL106_04_wza,KL106_06_wzc,KL106_08,KL106_10_wecB,KL106_13_wzx,KL106_17
O_locus: unknown (O1/O2v2)
O_type: unknown (O2afg)
O_locus_problems: ?-
O_locus_confidence: None
O_locus_identity: 98.38%
O_locus_missing_genes: O1/O2v2_05_wbbN,O1/O2v2_06_wbbO,O1/O2v2_07_kfoC,O1/O2v2_08_gmlC,O1/O2v2_09_gmlB,O1/O2v2_10_gmlA
AGly_acquired: aac(6')-Ib'.v1;aph3-Ia.v1^
Phe_acquired: catA1^
Sul_acquired: sul1
Tmt_acquired: dfrA12
Bla_acquired: TEM-1D.v1^
Bla_ESBL_acquired: SHV-12^
Bla_Carb_acquired: KPC-2
SHV_mutations: 238S;240K;35Q
Omp_mutations: OmpK35-25%
Flq_mutations: GyrA-83I;ParC-80I
truncated_resistance_hits: aadA2*-54%
spurious_resistance_hits: SHV-73*?-0%
ybtS: 6
ybtX: 4
ybtQ: 20
ybtP: 14
ybtA: 1
irp2: 30-71%
irp1: 30-14%
ybtU: 13
ybtT: 4
ybtE: 15
fyuA: 16-42%

Analysis performed: 2024-02-09; Kleborate v2.3.2

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