Environmental metagenomics and associated functional annotations in the polluted ecosystem: Antimicrobial resistance perspective

The emergence of antimicrobial resistance (AMR) is a critical threat to the environment and public health. The major sources contributing to the emergence of AMR in the environment are partially treated as well as untreated wastewater from hospitals, industries, and municipal treatment plants. While antibiotic usage in livestock, poultry, and aquaculture, as well as sludge and animal waste manure usage in agriculture, are the major drivers of AMR. Understanding the distribution and diversity of AMR genes in environmental samples is essential for designing effective mitigation strategies. Metagenomic analysis provides a powerful tool for identifying and characterizing AMR genes in complex microbial communities. This article highlights the importance of environmental AMR and discusses the tools and techniques used for metagenomic analysis. Recent studies have investigated AMR in various environmental samples, including wastewater, surface water, brackish water, and other sources. Metagenomics combined with bioinformatics analysis is a powerful ARG surveillance tool. These tools and databases are essential for the metagenomic analysis of AMR and provide a basis for any AMR study in metagenomics. They facilitate the identification and characterization of AMR genes in complex microbial communities, enabling researchers to understand better the distribution and diversity of AMR in the environment. In addition, metagenomic data can be used to devise and implement discharge standards, treatment, and mitigation strategies. The potential of metagenomic data for developing mitigation strategies and outlining future perspectives in this area provides insights into the existing state of research on environmental AMR and emphasizes the need for continued monitoring and surveillance to address this pressing public health challenge.