ABSTRACT
Antimicrobial resistance (AMR) is a growing public health concern worldwide, and metagenomics is an increasingly important tool for monitoring and understanding the spread of resistance genes in different environments. In the context of AMR, metagenomics can be used to track the presence of resistance genes in different environments, including those that are associated with human or animal use of antibiotics, as well as those that are naturally occurring. This information can provide insights into the sources and transmission of resistance genes and provides a valuable tool for monitoring and understanding the spread of resistance genes in efforts to combat the rise of AMR. Most microorganisms acquire antibiotic resistance genes (ARGs) through horizontal gene transfer (HGT), which are encompassed by the resistome. Therefore, recognizing and comprehending HGTs can offer valuable knowledge regarding the means by which antimicrobial resistance spreads and propagates. The current standard methods for identifying antibiotic-resistant bacteria rely on culture-based techniques. Nonetheless, certain resistance genes, including those in free-floating DNA, exist beyond the bacterial genome, which may be transferred upon antibiotic exposure. In contrast, metagenomic and metatranscriptomic profiling methods for detecting antibiotic resistance offer various benefits, such as an increased likelihood of identifying resistance genes inside and outside the bacterial genome and novel resistance genes. Several tools with varying capabilities, such as read-based and assembly-based tools, have been developed to identify antimicrobial resistant genes in a variety of the samples. This chapter aims to elucidate some of the recent methods used for metagenomic studies of antimicrobial resistant organisms and antimicrobial resistant genes.
