Harnessing eDNA Methodologies for Enhanced Surveillance of Antimicrobial Resistance Genes in Agricultural Soil: A Review

Abstract

Antimicrobial resistance (AMR) presents a notable catholic threat to animal and human health, with agricultural soil avowed as a major source of antibiotic resistance genes (ARG). The significant impact of anthropoid activities on the soil resistome is well-documented; a knowledge gap persists regarding certain microbial communities that confer resistance, along with the most efficacious methods for their monitoring. This review addresses the disparaging need for advanced, culture-based techniques to monitor ARGs in agricultural landscapes. We bring forth a broad-based overview of the methodologies and bioinformatic pipelines for using environmental DNA (eDNA) and metagenomics to snoop AMR. eDNA-based approaches are underscored for their cost-effectiveness, enhanced sensitivity, and non-invasive nature for detecting a wider scope of ARGs, as well as those from non-viable cells and mobile genetic elements, which repeatedly go undetected by traditional techniques. We moot how high-throughput sequencing of eDNA, incorporated with metagenomic analysis, permits a circumstantial assessment of the soil resistome, revealing both known and novel ARGs. We traversed the potential of these methodologies to bring forth subtle insights into ARG dynamics. This review rules that adopting a standardized eDNA metagenomics approach is key for effecting comparable, reliable data, through strengthening our understanding of AMR transmission via the soil-microbe-plant linkages and informing an effective public health blueprint to combat the post-antibiotic era.