title: Genotyping DNA chip for the simultaneous assessment of antibiotic resistance and pathogenic potential of extraintestinal pathogenic Escherichia coli.
abstract: Urinary tract infections (UTIs) are among the most frequently occurring infections and are mostly caused by extraintestinal pathogenic Escherichia coli. DNA microarrays are potent molecular diagnostic tools for rapid diagnosis of bacterial infections with high relevance for UTIs. In this study, we present the integration and application of two DNA chip modules for the simultaneous detection of single nucleotide polymorphisms in gyrA (quinolone resistance) and fimH (increased adhesion to urinary tract epithelium). The performance of the combined diagnostic chip was assessed by genotyping 140 E. coli strains. Resistance-causing mutations could only be identified in UTI isolates. A complete genotyping assay could be performed in <4h after DNA extraction. Together with the excellent genotyping results, this constitutes a competitive alternative as a standard tool for routine clinical diagnostics.
authors.affiliation: Division of Pathway Medicine, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK.
authors.forename: Timo
authors.initials: T
authors.lastname: Barl
authors.forename: Ulrich
authors.initials: U
authors.lastname: Dobrindt
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Yu
authors.forename: Don J
authors.initials: DJ
authors.lastname: Katcoff
authors.forename: David
authors.initials: D
authors.lastname: Sompolinsky
authors.forename: Stéphane
authors.initials: S
authors.lastname: Bonacorsi
authors.forename: Jörg
authors.initials: J
authors.lastname: Hacker
authors.forename: Till T
authors.initials: TT
authors.lastname: Bachmann
mesh_terms: D027081:DNA Gyrase / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000145:classification / Q000187:drug effects / Q000235:genetics / Q000472:pathogenicity; D004927:Escherichia coli Infections / Q000382:microbiology*; D029968:Escherichia coli Proteins / Q000235:genetics; D036781:Fimbriae Proteins; D020869:Gene Expression Profiling; D005838:Genotype; D006801:Humans; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D014552:Urinary Tract Infections / Q000382:microbiology*; D014774:Virulence / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; C063055:fimbrillin; D036781:Fimbriae Proteins; D027081:DNA Gyrase