A novel high-throughput method for molecular serotyping and serotype-specific quantification of Streptococcus pneumoniae using a nanofluidic real-time PCR system.
Serotype-specific quantification data are essential for elucidating the complex epidemiology of Streptococcus pneumoniae and evaluating pneumococcal vaccine efficacy. Various PCR-based assays have been developed to circumvent the drawback of labour-intensive and time-consuming culture-based procedures for serotype determination and quantification of pneumococcus. Here, we applied a nanofluidic real-time PCR system to establish a novel assay. Twenty-nine primer pairs, 13 of which were newly designed, were selected for the assay to cover 50 serotypes including all currently available conjugate and polysaccharide vaccine serotypes. All primer pairs were evaluated for their sensitivity, specificity, efficiency, repeatability, accuracy and reproducibility on the Fluidigm Biomark HD System, a nanofluidic real-time PCR system, by drawing standard curves with a serial dilution of purified DNA. We applied the assay to 52 nasopharyngeal swab samples from patients with pneumonia confirmed by chest X-ray to validate its accuracy. Minimum detection levels of this novel assay using the nanofluidic real-time PCR system were comparable to the conventional PCR-based assays (between 30 and 300 copies per reaction). They were specific to their targets with good repeatability (sd of copy number of 0.1), accuracy (within ±0.1 fold difference in log10 copy number) and reproducibility (sd of copy number of 0.1). When artificially mixed DNA samples consisting of multiple serotypes in various ratios were tested, all the serotypes were detected proportionally, including a minor serotype of one in 1000 copies. In the nasopharyngeal samples, the PCR system detected all the culture-positive samples and 22 out of 23 serotypes identified by the conventional method were matched with PCR results. We conclude that this novel assay, which is able to differentially quantify 29 pneumococcus groups for 45 test samples in a single run, is applicable to the large-scale epidemiological study of pneumococcus. We believe that this assay will facilitate our understanding of the roles of serotype-specific bacterial loads and implications of multiple serotype detections in pneumococcal diseases.
Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Japan.
Bhim Gopal
BG
Dhoubhadel
Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Japan.
Michio
M
Yasunami
Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Japan.
Lay-Myint
LM
Yoshida
Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
Hien Anh Nguyen
HAN
Thi
Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
Thu Huong Vu
THV
Thi
Department of Microbiology, Khanh Hoa General Hospital, NhaTrang, Vietnam.
Thuy Ai Nguyen
TAN
Thi
Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Japan.
Kiwao
K
Watanabe
Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Japan.
Motoi
M
Suzuki
Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Japan.
Konosuke
K
Morimoto
Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
Duc Anh
DA
Dang
Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Japan.
Koya
K
Ariyoshi
D017931:DNA Primers / Q000235:genetics; D006801:Humans; D044085:Microfluidics / Q000379:methods*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012703:Serotyping / Q000379:methods*; D013290:Streptococcal Infections / Q000175:diagnosis / Q000382:microbiology*; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
D017931:DNA Primers