A Head-to-Head Comparison of Two Microfluidic Digital PCR Platforms for Fecal Contamination Testing in Surface Waters

Given the lack of publications establishing the comparability of dPCR measurements for water quality assessment, we performed a robust comparison of QIAcuity and Absolute Q dPCR platforms for detecting and quantifying HF183/BacR287, Entero1a, and EC23S857 using a certified reference material (SRM 2917) and environmental water samples (n = 10). For experiments with SRM 2917, both platforms demonstrated very strong qualitative and quantitative agreement (intraclass correlation coefficients, ICC >0.96) with comparable precision down to 1.5–1.8 log10 GC/reaction (coefficient of variation <30%) and comparable 95% LODs for each assay (range 4.5–10 GC/reaction). During experiments with water samples, both platforms demonstrated strong repeatability among dPCR replicates both within and between platforms (Pearson's correlation coefficient >0.95) and strong quantitative agreement (ICC >0.84). However, QIAcuity detected HF183/BacR287 more frequently than Absolute Q when results were considered at the dPCR technical replicate (p = 0.0005) or filter replicate level (p = 0.0020) and target abundance was less than 100 GC/100 mL. Nonetheless, in the context of the large uncertainties inherent to interpreting and applying molecular data for water quality management, we conclude that for the assays considered, QIAcuity and Absolute Q would not lead to meaningfully different quantification.