Antibiotics and probiotics impact gut antimicrobial resistance gene reservoir in COVID-19 patients. human fecal metagenome

The coronavirus 2019 (COVID-19) pandemic has affected antimicrobial stewardship activities and driven AMR in various ways due to empirical use of antibiotics and increasing secondary bacterial infections among patients with COVID-19. Studies and meta-analysis have shown that approximately three quarters of patients with COVID-19 received antibiotics but only less than 10% had bacterial or fungal co-infections. We hypothesise that patients with COVID-19 have a high risk of ARGs accumulation and that probiotic therapy may have a role in reducing the resistome in these COVID-19. In this study, we performed longitudinal metagenomic analysis of fecal samples of 142 patients with COVID-19 and characterized the dynamics of ARGs reservoir from admission to 6 months after viral clearance.