Maternal vaginal colonization screening for term singleton pregnancy: comparative evaluation of metagenomic next-generation sequencing (mNGS) versus real-time quantitative PCR (qPCR).

Objective: To investigate the distribution characteristics of potential high-risk pathogens for early-onset neonatal infection in maternal vaginal secretions, and to perform a head-to-head comparative evaluation of detection performance for target pathogens between metagenomic next-generation sequencing (mNGS) and real-time quantitative polymerase chain reaction (qPCR), with conventional bacterial culture as the reference standard. Methods: A total of 294 valid maternal vaginal secretion samples were prospectively collected and tested in parallel using qPCR, mNGS, and conventional bacterial culture. The Chi-square test was used to compare the differences in pathogen detection rates among the three methods. Receiver operating characteristic (ROC) curve was plotted to calculate the area under the curve (AUC) and 95% confidence interval (CI), to systematically evaluate the detection performance of the two methods for target pathogens. Results: The spectrum of potential early-onset neonatal pathogens in maternal vaginal secretions, ranked by detection rate, was as follows: Conclusion: This head-to-head comparative study confirms that both mNGS and targeted qPCR have high accuracy and consistency for detecting potential early-onset neonatal pathogens in maternal vaginal secretions. We propose a tiered antenatal screening strategy for maternal vaginal pathogenic colonization: qPCR is recommended as the first-line tool for routine antenatal screening due to its high cost-effectiveness and rapid turnaround time, while mNGS is reserved for high-risk pregnant women (e.g., preterm premature rupture of membranes, clinical chorioamnionitis), culture-negative suspected infection cases, or scenarios requiring comprehensive pathogen profiling, to take full advantage of its unbiased, broad-spectrum detection capability. This integrated screening strategy requires further prospective validation with paired neonatal clinical outcome data to confirm its value in the prevention and early intervention of early-onset neonatal infection.