Design and Evaluation of Multiplex One-Step Reverse Transcription PCR–Dipstick Chromatography Method for the Analysis of Seven Respiratory Pathogens

• Published in: Current microbiology 2021-10, Vol.78 (10), p.3656-3666
• Main Authors: Luo, Li, Chen, Qianming, Qin, Sheng, Luo, Qiang, Liu, Zhenjie, Li, Qiong, Zheng, Shuilan, Huang, Xianzhang, Ke, Peifeng, Yang, Xiangsheng, Xiao, Hui, Xu, Ning
• Format: Article
• Language: English
• Subjects: Biomedical and Life Sciences; Biotechnology; Biotin; Chromatography; Coronaviruses; COVID-19; Deoxyribonucleic acid; Design analysis; DNA; Gene sequencing; Humans; Hybridization; Influenza; Influenza A; Influenza B; Latex; Life Sciences; Microbiology; Multiplex Polymerase Chain Reaction; Multiplexing; Nucleotide sequence; Oligonucleotides; Pathogens; Pneumonia; Polymerase chain reaction; Primers (coatings); Respiratory diseases; Respiratory syncytial virus; Respiratory tract; Respiratory tract diseases; Reverse Transcription; SARS-CoV-2; Sensitivity analysis; Sensitivity and Specificity; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Streptavidin; Viral diseases
• ISSN: 0343-8651; 1432-0991
• DOI: 10.1007/s00284-021-02621-7

Influenza A, influenza B, severe acute respiratory syndrome coronavirus 2, adenovirus, respiratory syncytial virus, Mycoplasma pneumoniae , and Chlamydophila pneumoniae are common pathogens that can cause severe pneumonia and other symptoms, resulting in acute lower respiratory tract infections. The objective of this study was to design and evaluate a sensitive and specific multiplex one-step reverse transcription PCR (RT-PCR)–dipstick chromatography method for simultaneous rapid detection of these seven pathogens. Streptavidin-coated blue latex particles were used to read out a positive signal. Based on the DNA–DNA hybridization of oligonucleotide sequences (Tag) for forward primer with the complementary oligonucleotide sequence (cTag) on the dipstick and biotin–streptavidin interactions, PCR products were able to be illuminated visually on the dipstick. The specificity and the limit of detection (LOD) were also evaluated. Moreover, the clinical performance of this method was compared with Sanger sequencing for 896 samples. No cross reaction with other pathogens was found, confirming the high specificity of this method. The LOD was 10 copies/µL for each of the tested pathogens, and the whole procedure took less than 40 min. Using 896 samples, the sensitivity and specificity were shown to be no lower than 94.5%. The positive predictive value was higher than 82.1%, and the negative predictive value was higher than 99.5%. The kappa value between the PCR–dipstick chromatography method and Sanger sequencing ranged from 0.869 to 0.940. In summary, our one-step RT-PCR–dipstick chromatography method is a sensitive and specific tool for rapidly detecting multiplex respiratory pathogens.