Analysis of 90,291 stool samples from symptomatic patients revealed dramatic differences in pathogen detection between molecular and traditional methods. PCR identified nearly five times more Aeromonas infections (2.9% vs 0.5%) and 35% more Campylobacter cases compared to bacterial culture, though slightly fewer Salmonella cases. Most striking was that 82% of PCR-positive Aeromonas samples showed no growth on culture plates, suggesting this waterborne pathogen is vastly underdiagnosed in clinical practice. This detection gap has significant implications for gastrointestinal diagnostics and public health surveillance. Aeromonas infections, often dismissed as rare, may actually represent a substantial burden of unrecognized illness, particularly given the age-related patterns observed—higher bacterial loads in older patients suggest increased vulnerability in aging populations. The discordance between methods likely reflects PCR's ability to detect non-viable organisms, fastidious strains, or low-density infections that culture methods miss. For clinical laboratories transitioning to molecular diagnostics, these findings underscore the need to recalibrate expectations about pathogen prevalence. The research also highlights how surveillance data quality depends heavily on detection methodology, with culture-based historical data potentially underestimating true disease burden for certain enteric pathogens.