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.Quinolones are among the most potent antibacterial agents used in human therapy. Fluoroquinolones have been widely applied as broad-spectrum antimicrobial agents in clinical medicine since 1983. With the worldwide use of this drug, the corresponding resistance among bacteria has increased significantly. One of the most relevant species is Escherichia coli, in particular for urinary tract infections, where E. coli is the infection-causing pathogen in 80% of cases. In clinical routine, 90% of these kinds of infections are treated with quinolone antibiotics. However, 7 to 9% of the pathogenic E. coli isolates are quinolone resistant and cause clinical complications (M. Susa, unpublished data). In addition, quinolone-resistant E. coli could be a potential threat to neutropenic patients with leukemia who receive a quinolone as prophylaxis (36). The molecular background of quinolone resistance is missense mutations (single-nucleotide exchanges) in the target enzyme genes and, less importantly, the reduction of quinolone accumulation inside the cells (2,10,16,22,27). In gram-negative organisms, such as E. coli, the primary target of fluoroquinolones is the DNA gyrase (3, 11). Missense mutations in the A subunit of the DNA gyrase are commonly considered to be the main reason for quinolone resistance in E. coli (8,9,28,30). Such single-nucleotide exchanges are clustered in a small region called the quinolone resistance-determining region (QRDR) (5, 27, 37). Up to now, the standard methods to determine antibiotic resistance, e.g., disk diffusion tests or Etests, have been based on phenotypic identification; these methods are time-consuming, are culture-based, and have room for improvement in terms of sensitivity and precision. A rapid and precise genotype-based diagnostic resistance test would be of great value for the clinic. Although several molecular genetic methods, such as single-stranded conformational polymorphi...