A fully automatic dPCR microfluidic system for detection of large-volume and low-abundance bacteria sample

Digital polymerase chain reaction (dPCR) has become a key technology for bacteria detection with superior sensitivity and accuracy, enabling in reducing the spread of waterborne disease. However, the current systems lack a complete dPCR detection workflow for low-abundance bacteria water sample in large-volume, including bacteria enrichment, nucleic acid (NA) extraction and digital arrays generation. In this work, a fully automated workflow system has been developed for dPCR detection. A preprocessing cartridge designed for single-use has been fabricated to realize the bacterial capture (∼ 98%), NA absorption (∼ 81%), mixing and heating. A PDMS-based microfluidic chip and a vacuum cover are employed for the generation of digital arrays without the pre-degas of PDMS. The proposed system exhibits a good linear relationship of Escherichia coli (E. coli) detection within the range from 2.5 × 101 CFU/mL to 2.5 × 104 CFU/mL, with a limit of detection ∼ 2.5 CFU/mL when enrich 5 mL sample. Furthermore, the dPCR detection results of four actual water samples are comparable to those obtained by the gold standard method plate counting, demonstrating its potential as a point-of-care testing (POCT) tool for accurate quantification of large-volume and low-abundance bacteria samples.