title: Direct detection and genotyping of Klebsiella pneumoniae carbapenemases from urine by use of a new DNA microarray test.
abstract: Klebsiella pneumoniae carbapenemases (KPCs) are considered a serious threat to antibiotic therapy, as they confer resistance to carbapenems, which are used to treat extended-spectrum beta-lactamase (ESBL)-producing bacteria. Here, we describe the development and evaluation of a DNA microarray for the detection and genotyping of KPC genes (bla(KPC)) within a 5-h period. To test the whole assay procedure (DNA extraction plus a DNA microarray assay) directly from clinical specimens, we compared two commercial DNA extraction kits (the QIAprep Spin miniprep kit [Qiagen] and the urine bacterial DNA isolation kit [Norgen]) for the direct DNA extraction from urine samples (dilution series spiked in human urine). Reliable single nucleotide polymorphism (SNP) typing was demonstrated using 1 × 10(5) CFU/ml urine for Escherichia coli (Qiagen and Norgen) and 80 CFU/ml urine, on average, for K. pneumoniae (Norgen). This study presents, for the first time, the combination of a new KPC microarray with commercial sample preparation for detecting and genotyping microbial pathogens directly from clinical specimens; this paves the way toward tests providing epidemiological and diagnostic data, enabling better antimicrobial stewardship.
authors.affiliation: Division of Pathway Medicine, University of Edinburgh, Medical School, Edinburgh, United Kingdom.
authors.forename: Harald
authors.initials: H
authors.lastname: Peter
authors.forename: Kathrine
authors.initials: K
authors.lastname: Berggrav
authors.forename: Peter
authors.initials: P
authors.lastname: Thomas
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Pfeifer
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Witte
authors.forename: Kate
authors.initials: K
authors.lastname: Templeton
authors.forename: Till T
authors.initials: TT
authors.lastname: Bachmann
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D004756:Enterobacteriaceae Infections / Q000382:microbiology*; D004926:Escherichia coli; D006801:Humans; D007711:Klebsiella pneumoniae / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D014556:Urine / Q000382:microbiology*; D001618:beta-Lactamases / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D001618:beta-Lactamases; C063912:carbapenemase