title: Development and validation of a diagnostic DNA microarray to detect quinolone-resistant Escherichia coli among clinical isolates.
abstract: The incidence of resistance against fluoroquinolones among pathogenic bacteria has been increasing in accordance with the worldwide use of this drug. Escherichia coli is one of the most relevant species for quinolone resistance. In this study, a diagnostic microarray for single-base-mutation detection was developed, which can readily identify the most prevalent E. coli genotypes leading to quinolone resistance. Based on genomic sequence analysis using public databases and our own DNA sequencing results, two amino acid positions (83 and 87) on the A subunit of the DNA gyrase, encoded by the gyrA gene, have been identified as mutation hot spots and were selected for DNA microarray detection. Oligonucleotide probes directed against these two positions were designed so that they could cover the most important resistance-causing and silent mutations. The performance of the array was validated with 30 clinical isolates of E. coli from four different hospitals in Germany. The microarray results were confirmed by standard DNA sequencing and were in full agreement with phenotypic antimicrobial susceptibility testing.
authors.affiliation: Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany.
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Yu
authors.forename: Milorad
authors.initials: M
authors.lastname: Susa
authors.forename: Cornelius
authors.initials: C
authors.lastname: Knabbe
authors.forename: Rolf D
authors.initials: RD
authors.lastname: Schmid
authors.forename: Till T
authors.initials: TT
authors.lastname: Bachmann
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D024881:Drug Resistance, Bacterial; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000382:microbiology; D005838:Genotype; D006801:Humans; D009154:Mutation / Q000235:genetics; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015363:Quinolones
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D015363:Quinolones