Toward Accurate and Robust Environmental Surveillance Using Metagenomics.

Jiaxian Shen,Erica M Hartmann,Mary K Hayden,Alexander G Mcfarland,Vincent B Young

doi:10.3389/fgene.2021.600111

Abstract

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.

Highlights

56% of the world’s population lives in urban areas (United Nations, 2018) and people in developed nations spend at least 90% of the time indoors (Chau et al, 2002; Smith et al, 2016; Cincinelli and Martellini, 2017), making built environments hotspots with which humans frequently interact
We focus on three critical conceptual and technical advances that need to be incorporated throughout the metagenomic environmental surveillance process: viability assessment, taxonomic resolution, and quantitation (Figure 1A)
Given the inherent nature of metagenomic shotgun sequencing that a fixed total number of reads are distributed based on the relative proportion of genetic materials present in a batch, limit of detection (LoD) must be approximated with the microbial community to be sequenced at a batch-based pace

Summary

Introduction

56% of the world’s population lives in urban areas (United Nations, 2018) and people in developed nations spend at least 90% of the time indoors (Chau et al, 2002; Smith et al, 2016; Cincinelli and Martellini, 2017), making built environments hotspots with which humans frequently interact. We focus on three critical conceptual and technical advances that need to be incorporated throughout the metagenomic environmental surveillance process: viability assessment, taxonomic resolution, and quantitation (Figure 1A). Low-biomass samples can be more susceptible to technical factors including library size, community complexity, host DNA, and contamination.

Results

Conclusion