Profile surveillance and risk assessment of the environmental dimension of antibiotic resistance via the metagenomic approach

Antibiotic resistance has been recognized as a global environmental and public health challenge. Over the past decades, methods of studying antibiotic resistance genes (ARGs) have rapidly evolved. This review summarizes progress in metagenomic approaches for profiling ARGs, mobile genetic elements (MGEs), and their microbial hosts. The transition from second-generation to third-generation sequencing technologies, developments in ARG detection pipelines, and emerging strategies for absolute quantification are highlighted. In addition, novel approaches for linking ARGs to their hosts and assessing resistome risks at both gene and sample levels are discussed. Continuous improvements in methodologies are deepening the understanding of resistance dissemination, and providing a foundation for environmental surveillance and risk control.