Long term prediction and prevention of known and emerging biological hazards for animal and human health testing microbiomes circulating in sewage

Climate change and global warming are causing catastrophic effects to humans, animals, and ecosystems, including the emergence of new biological hazards due to altered habitats, zoonotic spillover, and release of ancient pathogens. Current infection tracking methods face challenges such as overlooking asymptomatic cases and delays in data. Sewage surveillance, successfully employed during the COVID-19 pandemic, has proven effective as an early warning system for detecting infectious agents, reflecting the microbiome of a community. My PhD project investigates wastewater analysis for monitoring and predicting emerging biological hazards, particularly in the context of climate change, as highlighted by the EFSA report. Two experimental studies were conducted: one in Bologna, Italy, and another in Nantes, France. A longitudinal study in Bologna used shotgun metagenomics to map the sewage microbiome, identify pathogens, and correlate findings with climatic data. Within the VEO project, seasonal and environmental impacts on microbial communities were explored by recovering genomes directly from metagenomic data. In France, sewage and shellfish samples were analysed in collaboration with IFREMER to characterize the virome. Various next-generation sequencing protocols were tested to optimize detection of foodborne viruses in complex environmental matrices. A literature review further explored the integration of sewage and clinical data to identify foodborne pathogens and strengthen outbreak prevention. The sequencing analysis of sewage samples from the Bologna wastewater treatment plant revealed a dominant presence of Escherichia coli and fluctuating levels of Salmonella enterica and Vibrio cholerae. In France, a specific RNA sequencing workflow was most effective for strain-level viral differentiation. Case studies suggest sewage surveillance can monitor foodborne pathogens and detect trends exceeding baseline thresholds, offering a valuable preventive tool. The research highlights the potential of sewage-based surveillance for monitoring enteric viruses and microbial diversity in environmental and food samples, despite challenges with metagenomic variability and microorganism classification.