We established a real-time PCR assay with melting curve analysis to rapidly genotype quinolone resistancedetermining regions (QRDRs) of gyrase A and topoisomerase IV genes in Haemophilus influenzae. This assay is a useful tool for the detection of fluoroquinolone resistance and for the early detection of preexisting QRDR mutations.Haemophilus influenzae is a major causative pathogen isolated from infections, including acute and chronic respiratory infections, acute otitis media, sinusitis, and meningitis in pediatric patients. Recent reports have noted the prevalence of fluoroquinolone (FQ)-resistant H. influenzae (1,3,4,9,11,14,20,22,26). FQ-resistant H. influenzae often carries mutations in the quinolone resistance-determining regions (QRDRs) of the gyrA and the parC genes, which encode subunits of DNA gyrase and topoisomerase IV, respectively (9,11,16,18,23). A combination of real-time PCR methods and melting curve analysis (PCR-MCA) is a useful tool for the rapid detection of key gene mutations associated with drug resistance in various microorganisms (13,24,25), but there are no reports about H. influenzae. The aim of this study was to develop a PCR-MCA method for detecting H. influenzae strains by targeting a total of four QRDR positions in the gyrA (codons 84 and 88) and the parC (codons 84 and 88) genes that are frequently associated with FQ resistance (9,11,16,23). This current method could simultaneously identify the gyrA and the parC mutations by using only one PCR performance.Seventeen H. influenzae clinical isolates were used. Ten of the strains were susceptible to FQ, and seven of the strains had low susceptibility or were resistant to FQ. The seven FQresistant/low-susceptibility strains consisted of one strain (NUH-1) from Nagasaki University Hospital, one strain (BY-1) from Bayer (Osaka, Japan), two strains (DR-1 and DS-2) from Daiichi-Sankyo (Tokyo, Japan), and three strains (MSC24060, MSC27995, and MSC11438) kindly provided by Meiji-Seika Kaisha (Tokyo, Japan) (21). The 10 FQ-susceptible strains were isolated from patients at Nagasaki University Hospital. Identification of H. influenzae was confirmed by colony morphology, Gram staining, growth on chocolate agar, and the X and V factor requirements. The MICs of ciprofloxacin (CPFX), sparfloxacin, levofloxacin (LVFX), gatifloxacin, moxifloxacin, garenoxacin, and sitafloxacin were determined by a broth dilution method using Haemophilus test medium according to the recommendations of the Clinical and Laboratory Standards Institute (5). H. influenzae ATCC 51907 was used for quality control.DNA was extracted from each strain by using a QIAamp DNA mini-kit (Qiagen, Hilden, Germany). Sequences of the oligonucleotides and probes are shown in Tables 1 and 2. The sequences are from the known sequences of the parC and gyrA genes, which were derived from GenBank accession no. NP439678 and NP439419, respectively. To identify mutations in the QRDRs of gyrA and parC in these strains, we performed PCR and direct DNA sequencing according to the method described ...