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Life sciences · Journal article
Applied and Environmental Microbiology · October 7, 2026
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ABSTRACT Non-typhoidal Salmonella (NTS) poses a serious threat for multi-drug-resistant infections in the United States. However, most infections are not detected through traditional clinical surveillance, which severely underestimates the community disease burden. Wastewater-based epidemiology can overcome barriers in clinical surveillance and fill the gap. We performed a retrospective study to monitor disease trends and characterize viable NTS isolates from a medium-sized city’s wastewater treatment plants. Of 106 weekly raw influent samples from September 2020 to September 2021, 81 samples (76.42%) were NTS-positive via qPCR. NTS wastewater trends were a leading indicator of salmonellosis hospitalizations in the community by 1 week. The 27 unique NTS isolates (representing 11 different serotypes) recovered from wastewater revealed the biodiversity of community circulating infections. Wastewater samples showed a lower biodiversity of serotypes than environmental samples. The biodiversity of isolates collected from wastewater and clinical surveillance was similar but also represented serotypes not identified through traditional clinical surveillance approaches. Genotypic profiles of wastewater isolates revealed that many isolates have the potential for multi-drug-resistant infections and contain virulence genes associated with severe disease. This study shows that wastewater-based epidemiology is a valuable tool for monitoring disease trends and can provide early warning signs of salmonellosis in a community. We successfully enriched and cultured viable NTS isolates from raw wastewater samples frozen for over 1 year, further expanding the capabilities of retrospective studies allowing for future characterization of isolates. Overall, wastewater-based epidemiology is a powerful tool for retrospective analysis and for real-time community surveillance of NTS. IMPORTANCE Wastewater-based epidemiology (WBE) is an emerging tool for community-level infectious disease surveillance, yet its application to bacterial pathogens remains largely underexplored. Our study demonstrated that WBE effectively tracks non-typhoidal Salmonella (NTS) trends, serving as a leading indicator of hospitalizations. We successfully recovered and characterized Salmonella isolates from wastewater, highlighting its potential for genomic surveillance. We found that NTS remains viable in frozen wastewater samples for up to 1 year, the longest reported storage time to date. Characterizing bacterial isolates allows for studying pathogen evolution, AMR dynamics, and source tracking. Expanding WBE applications to bacteria could significantly enhance our understanding of disease dynamics and inform proactive public health interventions. Further research is needed to validate WBE as an early warning system for bacterial diseases and integration into a One Health framework. Our findings highlight WBE’s growing role in infectious disease epidemiology, reinforcing its value as a powerful public health surveillance tool.