Development of a New Rapid Simultaneous Molecular Assay for the Detection of STI Pathogens and Drug Resistance-Associated Mutations.

Background: In the diagnosis of sexually transmitted infections, there has been a demand for multiple molecular assays to rapidly and simultaneously detect not only pathogens but also drug resistance-associated mutations.

Methods: In this study, we developed a new rapid simultaneous molecular assay for the detection of Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis, Mycoplasma genitalium, and M. genitalium macrolide (23S rRNA gene, A2058/A2059) and fluoroquinolone (ParC gene, S83I) drug resistance-associated mutations in approximately 35 minutes. We evaluated the basic and prospective clinical performance of the newly developed assay.

Results: The newly developed assay showed sufficient sensitivity to detect N. gonorrhoeae, C. trachomatis, T. vaginalis, and M. genitalium relative to the reference method. In a prospective study comparing the reference method across 178 urine samples from men and women, the total concordance rate, sensitivity, and specificity of the two assays for N. gonorrhoeae detection were 98.9% (176/178), 97.9% (46/47), and 99.2% (130/131), respectively; for C. trachomatis detection, they were 98.3% (175/178), 96.4% (81/84), and 100% (94/94); and for M. genitalium detection, they were 100% (178/178), 100% (20/20), and 100% (158/158). All samples were negative for T. vaginalis. Of the 16 M. genitalium-positive samples analyzed for the GENECUBE assay, 81.3% (13/16) had A2058/A2059 mutations, 31.3% (5/16) had S83I mutations, and 25.0% (4/16) had simultaneous mutations, which was highly correlated with the sequence analysis.

Conclusions: This study suggests that the recently developed assay performed similarly to existing nucleic acid amplification tests and enables rapid and simultaneous detection, including the detection of drug resistance-associated mutations.