Food-residue-level antibiotics promote mucosal colonization of foodborne antibiotic-resistant Staphylococcus aureus in a simulated human gut

Antibiotic-resistant bacteria (ARB) and food-residue-level antibiotics in food can disrupt gut homeostasis. However, the impact of co-exposure with food-residue-level antibiotics on compartment-specific colonization dynamics and associated risks of ARB in human gut remains unclear. Here, we isolated a ciprofloxacin (CIP)-resistant Staphylococcus aureus strain from edible fish parts in aquaculture environment and assessed exposure risks to luminal and mucosal microbiotas using the in vitro Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME; ProDigest, Belgium) under three treatments: S. aureus alone, food-residue-level CIP alone, and co-exposure to both. Food-residue-level CIP promoted the potential colonization of S. aureus and relative abundance of antibiotic resistance gene hosts in the mucosal microbiota and decreased absolute abundance of 16S rRNA genes in luminal microbiota. Accordingly, microbiota exhibited compartment-specific responses: luminal microbiota exhibited increased stress tolerance potential and a tightly connected network with fewer nodes, whereas mucosal microbiota displayed enhanced resource utilization potential and a more complex network with more nodes. To investigate the mechanisms underlying these compartment-specific responses, we analyzed the microbial interconnections and enriched functions in luminal and mucosal microbiota. Notably, mucosal microbiota showed stronger positive cohesions (i.e., abundance-weighted positive correlations) within community members and enriched functions related to biofilm formation and quorum sensing, indicative of heightened communication and potential cooperation, possibly driving these compartment-specific responses. Despite these differences, continuous mucin shedding may facilitate the translocation of resistant mucosal biofilms, contributing to colonization resistance in the lumen. Our study demonstrates that food-residue-level antibiotics could facilitate S. aureus colonization and pose compartment-specific risks to gut microbial communities, highlighting the crucial role of intestinal mucosa for ARB colonization in human gut.