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Journal of Clinical Microbiology, September 2004, p. 4083-4091, Vol. 42, No. 9
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.9.4083-4091.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Development and Validation of a Diagnostic DNA Microarray To Detect Quinolone-Resistant Escherichia coli among Clinical Isolates

Institute of Technical Biochemistry, University of Stuttgart,¹ Department of Clinical Chemistry and Laboratory Medicine, Robert Bosch Hospital, Stuttgart, Germany²

Received 21 January 2004/ Returned for modification 17 March 2004/ Accepted 27 May 2004

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.

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