Integrated biological and chemical wastewater surveillance reveals local changes in dynamics of human-associated virus, bacteria and chemicals

Systematic analysis of environmental exposures ("exposomics") has become a major research focus in recent years, as it will enable comprehensive studies of the effect of changing environmental exposures on human health over time and between communities. Wastewater-based surveillance (WBS) is a well-established tool for community surveillance of pathogens and chemicals. During and after COVID-19 pandemic between July 2021 and May 2024 we systematically collected wastewater samples at 18 wastewater treatment plants covering 15 cities in Sweden and encompassing 41% of the national population. The sample set consisted of different seasons, different geographical areas with different climates ranging from sub-artic to temperate oceanic, and different classes of cities ranging from metropolitan to commuting cities. Wastewater samples were concentrated and biotic profiling analyzed using shotgun metagenomics and abiotic profiling using LC-MS/MS. From wastewater samples, we identified both known and unknown microbes, including human related bacteria and viruses, as well as sequences of unknown viral origin and a range of known and unknown environmental chemicals. We report a systematic detection of viral human pathogens and phages infecting bacteria typically found in human gut microbiota. Regional differences for both microbial and chemical exposome were identified. For two cities (Kalmar and Uppsala), we performed longitudinal sampling between 2022 and 2024 and found a high correlation of the bacterial, viral and chemical exposome in serial samples from the same city. Notably, there was consistently a 1.5-fold higher abundance of viruses in the wastewater of the city of Kalmar compared to Uppsala (PFDR=0.000007). This 1.5-fold higher abundance sustained across multiple human health-related pathogen species such as JC polyomavirus, gut bacteria infecting Carrus communis phages and Enterococcus faecalis bacteria. Seasonal changes in viral abundance in wastewater were also found (PFDR=0.001). Interestingly, we could also identify regional outbreaks of human infecting bacteria and virus such as Adenovirus F41 in Kalmar or changes in chemical abundance related to human activities and associated with the time of social relaxation of COVID-19 pandemic restrictions. In summary, systematic and integrated viral, bacterial, and chemical wastewater exposomics is a powerful tool for mapping of cumulative changes in human environmental exposures including unknown biological and chemical components and local outbreak features.