Vancomycin enhances VRE colonization and co-select for different ARGs classes in the human gut resistome

Antibiotic administrations are known to be one of the first cause of a dysbiotic microbiota, leading to several inflammatory diseases and enhancing the colonization of antimicrobial resistant (AMR) bacteria in the intestinal environment. In this study we used an in vitro continuous intestinal model PolyFermS to investigate the impact of different vancomycin doses and of a vancomycin-resistant Enterococci (VRE), Enterococcus faecium CCUG59168 (vanA, Tn1546-mediated, pVEF1 plasmid) alone or combined in the human gut microbiota. We evaluated the impact of antibiotic and strain on the complex gut community functionality (HPLC-RI), structure and diversity (qPCR and 16S rRNA metabarcoding), and on the resistome profile (shot-gun metagenomics). Our results showed the profound effects of vancomycin on the functionality and diversity of the human gut community. Furthermore, vancomycin was shown to enhance the colonization of the VRE strain. The modulation of the gut community by vancomycin resulted in co-selecting of several drug classes resistance ARGs, unrelated to the antibiotic, as fluoroquinolone and multidrug resistances mostly carried by few taxa, and which were the main driver of the resistome. Our results hint that exposure of the gut microbiota to vancomycin can increase resistome density. Moreover, we demonstrated that, when the microbiota is colonized by the VRE strain, vancomycin promotes the abundance of glycopeptide related resistance genes mediated by vanA gene cluster. In conclusion, our study revealed how the administration of vancomycin can re-shape the gut community and promote the opening of new niches to already present AMR bacteria that can proliferate and drive the resistome, enhancing the co-selection of specific resistance ARGs that are not related to vancomycin. Our data demonstrated the power of advanced in vitro continuous fermentation model such as PolyFermS for investigating the dynamics of AMR in gut microbiota subjected to antibiotics or other biotic or abiotic factors.