A portable pathogen analysis system (PPAS) designed to detect microbial pathogens at the point-of-sample collection. The system comprises a concentration tube used for the concentration of microbes in large volumes of water samples using super absorbent polymer (SAP) beads and a hand-powered centrifuge; and a processing component, which functions as a portable lab-on-a-disc droplet digital nucleic acid amplification system, which integrates DNA extraction, nucleic acid amplification, and post-amplicon analysis in a single unit. The present invention provides a fast, cost-effective, and user-friendly solution for microbial water quality analysis in low-resource settings.