Bacterial genomic DNA was prepared using the cetyltrimethylammonium bromide method (Ausubel et al., 1993). The purified DNA was quantified using the Nano Quant Infinite M200 spectrophotometer (Tecan, Männedorf, Proteases inhibitor Switzerland) at a wavelength of 260 nm. Primers and fluorescent dye-labeled TaqMan MGB probes were designed based on the nucleotide sequences that corresponded to the cps gene of S. pneumoniae (GenBank accession number NC_011072) obtained from SSH using the primer express 3.0 program (Applied Biosystems, Foster City, CA). The primer set cpsA-348F (5′-GCTGTTTTAGCAGATAGTGAGATCGA-3′) and cpsA-415R (5′-TCCCAGTCGGTGCTGTCA-3′)
defined an amplicon of 67 base pairs (bp). A carboxyfluorescein (FAM)-labeled probe cpsA-TaqMan FAM (5′-FAM-AATGTTACGCAACTGACGAG-MGBNFQ1-3′) was used for detection.
Standard curves and minimal limit of detection were generated by plotting the cycle threshold values (CT) of the qPCR performed on a dilution series of purified DNA from S. pneumoniae KCTC 5080T cells (107–1 CFU mL−1) against the log input cells mL−1. Streptococcus pneumoniae concentrations were calculated using a viable cell plate count method. Serial 10-fold dilutions of RXDX-106 cell line the cultures were inoculated on BHI agar (Difco Laboratories). The plates were subsequently incubated at 37 °C for 16 h, and cultural counts (in CFU) were determined in triplicate. The primer and probe concentrations for each of the three assays were optimized, and, in accordance with the experimentally optimized concentrations, 250 nM cpsA-specific primers and 150 nM cpsA-specific probes were used for all subsequent experiments. DNA was amplified with the 7300 real-time PCR system (Applied Biosystems) using the following cycling parameters: 95 °C for 10 min, followed by 50 cycles of 95 °C for 15 s
and 60 °C for 1 min. Amplification data were analyzed using sds software (7300 Real-time PCR System Sequence Detection Software v1.31, Applied Rho Biosystems). A specimen was considered positive if two of the three triplicates yielded a positive result within the <50-cycle cutoff. Conventional PCR-based methods have been developed to differentiate S. pneumoniae strains from the closely related viridans group streptococci. However, the lateral gene transfers that occur among the viridans group streptococci limit this differentiation, making it difficult to diagnosis S. pneumoniae in the human environment. In fact, some pneumococcal virulence genes of S. pneumoniae have been detected in S. mitis or S. oralis isolates (Whatmore et al., 2000; Verhelst et al., 2003; Seki et al., 2005). The cpsA gene was identified as a novel genomic marker specific to S. pneumoniae using the SSH technique, which allows accurate discrimination of S. pneumoniae from the closely related viridans group streptococci. In our study, a qPCR technique targeting the cpsA gene was developed to detect and enumerate the human pathogen, S.