Beyond the Test Result: A Two-Year Real-World Characterization of Quantitative Aspergillus PCR in a Tertiary Pulmonology Center

Background: Pulmonary aspergillosis remains underdiagnosed in patients with structural lung disease, as conventional methods might miss a part of cases. There are few real-world data on quantitative PCR performance outside immunocompromised populations. We evaluated the Aspergillus ELITe MGB Kit across two years of routine clinical practice at a tertiary pulmonology center. Methods: We retrospectively analyzed 492 consecutive ELITe MGB PCR tests (October 2023–September 2025) at the Marius Nasta Institute of Pneumology, Bucharest, Romania, performed on bronchoalveolar aspirate (n = 219), lavage (BAL; n = 202), and plasma (n = 65). Results were correlated with microscopy, fungal culture, imaging, and host risk factors where available. Results: Of 451 evaluable tests, 140 (31.0%) were significant, 7 (1.6%) low-level detected, and 304 (67.4%) non-significant or negative. Combined positivity was 32.6%. Aspirate outperformed BAL in positivity rate (42.8% vs. 30.8%; p ≈ 0.013); aspirate and BAL had similar median DNA loads (120 copies/mL each) but aspirate showed a longer tail toward very high loads (p < 0.001); raw median DNA loads (67 vs. 120 copies/mL) were not directly comparable between matrices due to differing matrix-specific lower limits of quantification (50 vs. 120 copies/mL, reflecting BAL dilution). Plasma positivity was 1.8%. Positivity peaked in May–June (42.5–45.5%), contrasting with the classical autumn pattern. Chronic obstructive pulmonary disease (COPD) was the dominant risk factor (OR = 3.45). PCR exclusively detected Aspergillus in the majority of cases where microscopy and culture were negative. Conclusions: The ELITe MGB kit demonstrates clinically meaningful diagnostic yield in a real-world pulmonology cohort. Aspirate consistently outperforms BAL, and the low-level detected category identifies a borderline population warranting prospective validation. The unexpected spring–summer positivity peak suggests a greater role for post-viral aspergillosis than previously recognized in this setting.