Multiplex-PCR Identification of Positive Blood Cultures: Pathogen Epidemiology, Resistance Determinants, and the Economic and Interpretive Cost of Qualitative Rapid Diagnosis

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Background/Objectives: Bloodstream infections (BSIs) carry high mortality, and any delay in initiating optimal antimicrobial therapy worsens outcomes. Syndromic multiplex-PCR panels applied to signal-positive blood cultures markedly shorten time-to-identification but are expensive and report results in a strictly qualitative format. We describe twenty-two months of real-world BioFire FilmArray Blood Culture Identification 2 (BCID2) testing in a southern Italian hospital, focusing on pathogen epidemiology, resistance-gene detection, and the economic and interpretive trade-offs of the assay. Methods: We retrospectively reviewed all BCID2 runs performed on signal-positive blood-culture bottles at P.O. “Vito Fazzi” (ASL Lecce) from July 2024 to April 2026. Each run was classified as single-pathogen-positive, polymicrobial (co-infection)-positive, or negative (no on-panel target). Resistance determinants were tabulated by year and by presumptive carrier. A direct-cost analysis was performed at a reagent cost of €250 per test. Results: Of 498 runs, 401 (80.5%) yielded at least one on-panel target (330 single-pathogen, 71 polymicrobial), whereas 97 (19.5%) were negative. Among 526 organism detections, Gram-positive (48.9%) and Gram-negative (45.8%) bacteria predominated; Staphylococcus spp., Escherichia coli and the Klebsiella pneumoniae group were most frequent. Resistance determinants (n = 244) were dominated by mecA/C, CTX-M and KPC. Co-infections (17.7% of positives) frequently prevented unambiguous attribution of a resistance gene to a specific co-detected organism. Total reagent expenditure was €124,500, of which €24,250 (19.5%) was spent on negative results. Conclusions: BCID2 delivered rapid, broad pathogen and resistance-gene detection in a high-resistance setting. Its qualitative-only output, the difficulty of attributing a resistance gene to a specific organism in polymicrobial samples, and the cost of negative results nonetheless argue for diagnostic-stewardship gating, semiquantitative reporting, and local validation of complementary and lower-cost assays.

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