Next-generation DNA sequencing has opened new possibilities for microbial water quality monitoring, particularly for addressing emerging concerns like antibiotic resistance and opportunistic pathogens.   Here we will demonstrate how the approach is being applied to survey antibiotic resistance genes and pathogen gene markers in various water and environmental systems, including drinking water, wastewater, reclaimed water, and agricultural manure management systems.  Current efforts are focused on deriving various metrics from metagenomic data for assessing presence of these targets and potential to spread undesirable traits, such as antibiotic resistance and virulence genes.  As DNA sequencing and bioinformatic technologies are rapidly developing, development and validation of various approaches is needed, along with adoption of standardized methods by relevant stakeholders.

Learning Objectives: 

1. Describe what shotgun metagenomic sequencing is and benefits for water analysis
2. Describe current limitations to shotgun metagenomic approaches for pathogen and resistance monitoring
3. Describe new developments and approaches for advancing metagenomic tools for water monitoring