Gut microbiome and antibiotic resistance effects during travelers' diarrhea treatment and prevention

International travelers are frequently afflicted by acute infectious diarrhea, commonly referred to as travelers' diarrhea (TD). Antibiotics are often prescribed as treatment or prophylaxis for TD; however, little is known about the impacts of these regimens on travelers' gut microbiomes and carriage of antibiotic resistance genes (ARGs). Here, we analyzed two cohorts totaling 153 US and UK servicemembers deployed to Honduras or Kenya. These subjects either experienced TD during deployment and received a single dose of one of three antibiotics [Trial Evaluating Ambulatory Therapy of Travelers' Diarrhea (TrEAT TD) cohort] or took once-daily rifaximin (RIF), twice-daily RIF, or placebo as prophylaxis to prevent TD [Trial Evaluating Chemoprophylaxis Against Travelers' Diarrhea (PREVENT TD) cohort]. We applied metagenomic sequencing on 340 longitudinally collected stool samples and whole-genome sequencing on 54 Escherichia coli isolates. We found that gut microbiome taxonomic diversity remained stable across the length of study for most treatment groups, but twice-daily RIF prophylaxis significantly decreased microbiome richness post-travel. Similarly, ARG diversity and abundance were generally stable, with the exception of a significant increase for the twice-daily RIF prophylaxis group. We also did not identify significant differences between the ARG abundance of E. coli isolates from the TrEAT TD cohort collected from different treatment groups or timepoints. Overall, we found no significant worsening of gut microbiome diversity or an increase in ARG abundance following single-dose treatment for TD, underscoring that these can be effective with low risk of impact on the microbiome and resistome, and identified the relative microbiome risks and benefits associated with the three regimens for preventing TD.