Development and application of a method to detect 27 respiratory pathogens using multiplex RT-PCR combined with MassARRAY technology.

BACKGROUND: Respiratory tract infections are the most common infections that lead to morbidity and mortality worldwide. Early recognition and precise diagnosis of microbial etiology is important to treat LRTIs promptly, specifically and effectively. OBJECTIVES: To establish a method based on multiplex reverse transcription (MRT)-PCR and MassARRAY technology for the simultaneous detection of 27 respiratory pathogens and explore its clinical application value. METHODS: Analytical sensitivity and specificity of the MRT-PCR-MassARRAY system were validated using inactivated bacterial and viral strains. Also we analyzed samples from 207 patients by MassARRAY methods and compared the results with consensus PCR/reverse transcription (RT)-PCR. RESULTS: The minimum detection limit of our MRT-PCR-MassARRAY method for pathogens was 10-100 copies/µl, with high specificity. Comparison test with consensus PCR/RT-PCR on 207 clinical samples, the positive, negative, and total correlation rates were 100, 98.68, and 99.03%, respectively. There was a high degree of agreement between the test results of the two methods (P < 0.01 by McNemar's test). CONCLUSION: Our detection system of 27 respiratory pathogens based on MassARRAY technology has high sensitivity and specificity, high throughput, and is simple to operate. It provides diagnostic value for the clinical diagnosis of respiratory pathogens and is of great significance in the screening of respiratory pathogens.

Detection and identification of bacterial pathogens directly from sputum samples by pyrosequencing.

PURPOSE: The standard culture findings for detecting and identifying bacterial pathogens in patients with lower respiratory tract infections (LRTIs) are usually not available for two to three days, which delays the initiation of appropriate antibiotic therapies. We aimed to develop a faster method of identification of bacterial pathogens in LRTIs which would offer a timelier guide to initial antibiotic choices. METHODOLOGY: The developed PCR-pyrosequencing-based method was defined as mask PCR-pyrosequencing (MPP). This method uses primer pairs deliberately designed to mask the interference of colonised bacteria in sputum to detect and identify bacterial pathogens directly from LRTI patient sputum samples within 5 h. Accordingly, the standard PCR-pyrosequencing method was defined as normal PCR-pyrosequencing (NPP) here. The clinical performance of the novel system was evaluated by comparing with traditional semi-quantitative culture and identification results. RESULTS: The coincidence for culture and MPP was 91.3 %. Compared with the semi-quantitative culture results, NPP identified 89.9 % strains of grade 3+ (corresponding to 1.0×106 c.f.u ml-1) and 100 % of grade 4+ (corresponding to 1.0×107 c.f.u ml-1), both of which were considered to be the presumptive pathogens in the clinics. MPP identified 98.9 % strains of grade 3+ and 100 % of grade 4+. Additionally, PCR-pyrosequencing could detect a minimum concentration of 1.0×106 c.f.u ml-1 of bacteria in sputum, with no significant difference between NPP and MPP. CONCLUSION: The PCR-pyrosequencing technique developed in this study is an accurate, fast, and high throughput method for the direct detection and identification of bacterial pathogens from sputum.

Development and validation of a multiplex reverse transcript real-time PCR for E6/E7 mRNA detection of high-risk human papillomavirus.

PURPOSE: Human papillomavirus (HPV) E6/E7 mRNA is a more specific marker for cervical lesion screening than HPV DNA. Here, we aimed to develop a new one-step multiplex reverse transcript real-time PCR (MRT-PCR) to detect E6/E7 mRNA from 14 high-risk HPV (hrHPV) genotypes. METHODOLOGY: The analytical sensitivity and specificity of the MRT-PCR system were validated. Its clinical performance was evaluated by comparing the results with bDNA signal amplification assay and histopathological results. RESULTS: The detection limit of MRT-PCR was 20 to 200 copies per reaction of different HPV genotypes, and no cross-reactivity was observed with any other low-risk HPV or other pathogens commonly found in the female genital tract. Using the bDNA signal amplification assay for comparison, a test on 166 clinical samples showed that the overall agreement between the two methods was 95.18 % and the one-step MRT-PCR was more sensitive. Further, compared with the histopathological results for the 166 clinical samples, the sensitivity and specificity of the MRT-PCR method were 88.9 and 71.6 %, respectively, and the positive rate for hrHPV E6/E7 mRNA increased with the severity of the cervical lesions. CONCLUSION: The one-step multiplex RT-PCR for E6/E7 mRNA detection is a simple, fast, universally applicable, sensitive and highly specific method for hrHPV E6/E7 mRNA detection. It is reliable for cervical lesion screening and of potential value in future clinical applications.

Development and validation of a method for human papillomavirus genotyping based on molecular beacon probes.

We describe a new assaying system for the detection and genotyping of human papillomavirus (HPV) based on linear-after-the-exponential-PCR(LATE-PCR) and melting curve analysis. The 23 most prevalent HPV strains (types 6, 11, 16, 18, 31, 33, 35, 39, 42, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73, 81, 82, and 83) are assayed in two sealed reaction tubes within 2 h. Good sensitivity and specificity was evaluated by testing cloned HPV DNA and clinical samples. The detection limit was 5-500 copies/reaction depending on the genotype. No cross-reactivity was observed with the other HPV types that are not covered by our method or pathogens tested which were commonly found in female genital tract. When compared with the HPV GenoArray Diagnostic kit, the results from 1104 clinical samples suggest good overall agreement between the two methods,(98.37%, 95% CI: 97.44%-98.97%) and the kappa value was 0.954. Overall, this new HPV genotyping assay system presents a simple, rapid, universally applicable, sensitive, and highly specific detection methodology that should be useful for HPV detection and genotyping, therefore, is potentially of great value in clinical application.