Internally controlled recombinase-aided amplification (IC-RAA) assays for the detection of human papillomavirus genotypes 16 and 18 using extracted DNA and samples treated with nucleic acid releasing agent

Development of Enzymatic Recombinase Amplification Assays for the Rapid Visual Detection of HPV16/18

Human papillomavirus (HPV) types 16 and 18 are the major causes of cervical lesions and are associated with 71% of cervical cancer cases globally. However, public health infrastructures to support cervical cancer screening may be unavailable to women in low-resource areas. Therefore, sensitive, convenient, and cost-efficient diagnostic methods are required for the detection of HPV16/18. Here, we designed two novel methods, real-time ERA and ERA-LFD, based on enzymatic recombinase amplification (ERA) for quick point-of-care identification of the HPV E6/E7 genes. The entire detection process could be completed within 25 min at a constant low temperature (35-43°C), and the results of the combined methods could be present as the amplification curves or the bands presented on dipsticks and directly interpreted with the naked eye. The ERA assays evaluated using standard plasmids carrying the E6/E7 genes and clinical samples exhibited excellent specificity, as no cross-reaction with other common HPV types was observed. The detection limits of our ERA assays were 100 and 101 copies/μl for HPV16 and 18 respectively, which were comparable to those of the real-time PCR assay. Assessment of the clinical performance of the ERA assays using 114 cervical tissue samples demonstrated that they are highly consistent with real-time PCR, the gold standard for HPV detection. This study demonstrated that ERA-based assays possess excellent sensitivity, specificity, and repeatability for HPV16 and HPV18 detection with great potential to become robust diagnostic tools in local hospitals and field studies.

Development of a duplex recombinase-aided amplification assay for direct detection of Mycoplasma pneumoniae and Chlamydia trachomatis in clinical samples

BACKGROUND

Pneumonia caused by Mycoplasma pneumoniae is common in the elderly and children, and pneumonia caused by Chlamydia trachomatis is prevalent in newborns. This study aimed to establish a rapid, sensitive, and simple method for the direct detection of M. pneumoniae and C. trachomatis in clinical samples without DNA extraction.

METHODS

We established a duplex recombinase-aided amplification (RAA) assay with the RNAseP gene as an internal control for detecting the P1 gene of M. pneumoniae and the ORF8 gene of C. trachomatis, respectively. The results were obtained at 39 °C within 15-20 min. A total of 130 clinical samples suspected of M. pneumoniae or C. trachomatis infection were collected and tested by duplex RAA and PCR. DNA extracted via a commercial kit or treated with a nucleic acid-releasing agent was used and compared, respectively. Standard recombinant plasmids were used to test the sensitivity of the duplex RAA assay. In addition, other similar common pathogens were used to verify the specificity of the duplex RAA assay.

RESULTS

The sensitivity of the duplex RAA assay for detecting M. pneumoniae and C. trachomatis was 10 copies/μL using recombinant plasmids. Compared with PCR, the sensitivity and specificity of duplex RAA assays for M. pneumoniae and C. trachomatis was 100% using clinical DNA samples extracted using a commercial kit and a nucleic acid-releasing agent, and the Kappa value was 1.

CONCLUSION

The advantages of this duplex RAA assay include high sensitivity and specificity, short duration, and simple extraction steps, with potential for use in the on-site detection of M. pneumoniae and C. trachomatis in resource-limited settings.

Development and evaluation of a sensitive recombinase aided amplification assay for rapid detection of Vibrio parahaemolyticus

Vibrio parahaemolyticus (V. parahaemolyticus) is a widely distributed pathogen in the coastal areas, which causes food poisoning and leads to gastroenteritis and sepsis. Therefore, developing a simple, sensitive, and rapid detection method for V. parahaemolyticus is a major concern globally. This study established a sensitive and rapid technique based on recombinase aided amplification (RAA) to detect V. parahaemolyticus. The RAA reaction was carried out successfully at 39 °C within 30 min. The sensitivity of the RAA assay was 10¹ copies/μL using the recombinant plasmid and 10^-3 ng/μL using the V. parahaemolyticus strain. In addition, RAA directly detected 7 × 10³ CFU/mL of simulated fecal samples and 0.1 CFU/mL after enrichment for 4 h. The sensitivity and specificity of the RAA assay using fecal and fish samples were 100% similar to that of the real-time PCR. We conclude that the RAA assay is an ideal screening method for detecting V. parahaemolyticus due to its rapidity, high accuracy, and simplicity in operation.