Comprehensive Diagnosis of Abnormal Vaginal Discharge Using qPCR-Based Microbial Dysbiosis Indices

Background/Objectives: Abnormal vaginal discharge (AVD) is a common complaint among women of reproductive age, often involving multiple, overlapping etiologies, most commonly bacterial vaginosis (BV), vulvovaginal candidiasis (VVC), aerobic vaginitis (AV), and sexually transmitted infections (STIs). We aimed to evaluate a syndromic diagnostic approach by developing qPCR-derived dysbiosis indices for BV, VVC, and AV, subsequently comparing their performance against established reference methods and clinician-assigned diagnoses. Methods: Vaginal swabs were collected in a case–control design from 74 symptomatic and 64 asymptomatic women at two clinics in Slovenia. Commercial qPCR assays quantified the microbial species associated with AVD. Relative abundances were integrated into novel dysbiosis indices. Diagnostic performance was validated against the Nugent scoring system (for BV), semiquantitative Candida culture with clinical symptoms (for VVC), and Hay–Ison criteria (for AV). Results: In this internally validated study, dysbiosis indices demonstrated high agreement with their respective reference tests and outperformed clinician-assigned diagnoses across all three conditions. The syndromic approach further revealed that mixed etiologies were frequent, leading to a diagnostic resolution for this patient subset. Conclusions: qPCR-based microbial dysbiosis indices offer a robust alternative to microscopy, particularly in settings where microscopy is not routinely performed. This method improves the accuracy of AVD evaluation and supports more targeted clinical management.