Rifamycin use and gut microbial antibiotic resistance genes in cirrhosis: Results from a double-blind, placebo-controlled clinical trial

Antimicrobial resistance gene (ARG) carriage is associated with poor outcomes in patients with liver cirrhosis, which is worsened by repeated antibiotic exposure and hospitalizations. While the semi-synthetic rifamycin derivative, rifaximin, has recently been linked to ARG expansion preclinically, the effects of rifamycin SV MMX (RiVM) on the gut resistome remain unknown. We evaluated longitudinal resistome changes with RiVM in cirrhosis. The randomized, double-blind, placebo-controlled RIVET trial (15 RiVM, 15 placebo) included compensated cirrhosis patients who underwent shotgun metagenomic sequencing before/after 30 days of therapy. ARGs were annotated using the Comprehensive Antibiotic Resistance Database. The longitudinal resistome was evaluated using univariable and multi-variable methods (LEfSe, paired-Wilcoxon testing, and MaAsLin3), and machine learning (ML) was used to determine ARG changes at subject and group levels. RiVM induced minimal perturbation of the gut resistome, without significant change in ARGs versus after FDR adjustment. Complementary approaches (univariable and multivariable) identified a trend towards lower vancomycin resistance ARGs, including vanW and vanT operon-associated genes, after RiVM exposure. In contrast, several Enterobacteriaceae-associated multidrug efflux regulators (including evgS, emrK, and mdtA) showed nominal increases post-rifamycin that did not withstand FDR. Group-level ML demonstrated limited discrimination between groups; however, within-subject longitudinal models achieved improved classification performance. No increase in infections or treatment-related safety concerns was observed. We conclude that rifamycin MMX was not associated with infections and did not enrich antimicrobial resistance genes compared to placebo in a small randomized 30-day clinical trial in patients with compensated cirrhosis. There was a tendency towards reduced vancomycin resistance and ARG reduction after rifamycin exposure. Registration: NCT04082780 www.clinicaltrials.gov