Fecal contamination of water supplies is a major cause of infectious disease with consequences ranging from minor illness to patient death. Current culture-based detection methods are decades old and take days to complete. Once identified, the presence of specific pathogens can take additional time. Clearly, the development of modern methods of detection are imperative. Automated polymerase chain reaction (PCR)-based methods would have major advantages over current procedures. The automation (1) minimizes risks of amplicon contamination and (2) allows for reliable, high throughput analysis. The PCR methodology (1) allows rapid turnaround time of hours instead of days, (2) permits adjustable sensitivity and specificity, (3) enables rapid subsequent analysis of positives samples to identify specific pathogens, and (4) identifies hard to culture pathogens. Such a system would help to minimize exposure to contaminated water sources and, when exposure has occurred, to rapidly guide appropriate antimicrobial chemotherapy, thus reducing morbidity and mortality.