Wastewater Surveillance

Wastewater surveillance is a method to detect, identify and characterize pathogens found in wastewater. This method provides data to help monitor outbreaks and other threats at the community level. By knowing where these threats are, communities can better allocate resources during a public health response. Genomic information from wastewater can be used to determine which pathogens are present in a community and identify what strains and how many variants may be in the community.

Wastewater surveillance is a vital tool for detecting and characterizing pathogens in sewage samples and treatment plants. When used with NGS-based technologies, wastewater surveillance can expand our understanding of many different pathogens, including RNA and DNA viruses, bacteria, and antimicrobial resistance (AMR) markers. This information is crucial for tracking the spread of many infectious diseases and developing effective responses.

Using samples from sewage, wastewater surveillance can help supplement existing surveillance methods and has several advantages, including:

• Population-based infection tracking
• Anonymous pooled testing
• Geographic information about disease spread
• Easy and rapid sampling that can be obtained as needed from treatment facilities to identify community-level trends

Wastewater samples usually contain multiple pathogens and microbes, as opposed to clinical samples which usually only contain a single pathogen. To analyze pathogens of interest, it is recommended to use amplicon- or enrichment-based NGS library preparation methods. Amplicon-based approaches use primers to specifically target regions of microbes and/or whole genomes of single viruses, while enrichment approaches use probe hybridization to capture genomes of interest. In addition, shotgun metagenomic sequencing provides a comprehensive method to analyze all genes and microbes within a sample.