Longitudinal Study of Antibiotic-Driven Resistome Changes and EARB Persistence in the Human Gut
Antibiotic overuse has driven the global spread of antimicrobial resistance (AMR), posing a significant threat to human health. While the environmental and clinical reservoirs of AMR genes (resistome) have been extensively studied, the functional roles and persistence of AMR bacteria within individuals remain poorly understood. This study investigates the strain-level dynamics of the human gut resistome following antibiotic treatment through a longitudinal metagenomic analysis. We reconstructed a large number of metagenome-assembled genomes (MAGs) from fecal samples of individuals undergoing antibiotic therapy. We identified two distinct populations of AMR bacteria based on their resistome profiles: extensively acquired antimicrobial resistant bacteria (EARB) and sporadically acquired antimicrobial resistant bacteria (SARB). Notably, EARB exhibited broader drug resistance and a significantly greater impact on shaping the post-antibiotic gut microbiome composition compared to SARB. Our findings reveal the importance of EARB in the persistence and spread of AMR within the human gut and highlight the need for strain-resolved analysis to fully understand the complex dynamics of the resistome. This study provides a deeper understanding of how antibiotic treatment shapes the human gut resistome at the strain level and offers novel insights into the ecological roles of EARB and SARB. The results contribute to developing strategies for controlling the spread of AMR bacteria in the human community.