Expanding a Wastewater-Based Surveillance Methodology for DNA Isolation from a Workflow Optimized for SARS-CoV-2 RNA...

Area of Science:

• Environmental microbiology
• Epidemiology
• Molecular biology

Background:

• Wastewater-based surveillance (WBS) is a valuable tool for monitoring infectious disease spread, primarily using RNA targets like SARS-CoV-2.
• Expanding WBS to include DNA pathogens requires adapting existing RNA-focused extraction protocols.

Purpose of the Study:

• To modify an RNA-specific wastewater extraction workflow for improved DNA isolation.
• To evaluate the impact of bead bashing on DNA and RNA recovery from wastewater.

Main Methods:

• Modified sample concentration and bead bashing steps in a standard RNA extraction workflow.
• Assessed DNA and RNA recovery using quantitative polymerase chain reaction (qPCR).

Main Results:

• Bead bashing significantly improved DNA recovery for bacterial targets (e.g., Mycobacterium) but reduced RNA recovery for viruses.
• qPCR quantification of RNA viruses was negatively impacted by bead bashing.

Conclusions:

• Separate WBS workflows are recommended: one without bead bashing for RNA viruses and one with bead bashing for DNA pathogen isolation.
• Existing SARS-CoV-2 WBS methods need reoptimization to broaden pathogen detection capabilities for public health.