Toward Accurate and Robust Environmental Surveillance Using Metagenomics

Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and the continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out in addressing the need. However, several hurdles remain to be overcome in order to generate actionable interpretations from metagenomic sequencing data for infection prevention. Conceptually and technically, we focus on viability assessment, taxonomic resolution, and quantitative metagenomics, and discuss their current advancements, necessary precautions and directions to further development. We highlight the importance of building solid conceptual frameworks and identifying rational limits to facilitate the application of techniques. We also propose the usage of internal standards as a promising approach to overcome analytical bottlenecks introduced by low biomass samples and the inherent lack of quantitation in metagenomics. Taken together, we hope this perspective will contribute to bringing accurate and consistent metagenomics-based environmental surveillance to the ground.

Automated summary

Environmental surveillance is crucial for combating public health threats like COVID-19 and antibiotic resistance. Metagenomics methods show promise but face obstacles in generating actionable interpretations. Focus on viability assessment, taxonomic resolution, quantitative metagenomics, and the use of internal standards is needed to advance the field and bring accurate monitoring to reality.