The incidence of multidrug resistant Enterobacteriaceae (MRE) is increasing worldwide. Infections from MRE can lead to diarrhea or bacteremia. While some intestinal bacterial commensals are known to oppose the colonization of MRE in the intestine, studies investigating the overall intestinal microbiota changes occurring in MRE-positive carriers are scarce. With my work, I analysed gut microbiota composition changes upon intestinal MRE intestinal acquisition, subsequent infection (e.g. diarrhea) and during anti-MRE therapies by next-generation sequencing technologies. This approach allowed me to bypass laboratory culturing as nucleic acids were directly extracted from stool samples. I showed association between microbiota composition, MRE intestinal loss and traveler's diarrhea. I reported that antibiotics were detrimental for microbiota irrespective of anti-MRE therapy duration, but these side effects were reversible when treatment was interrupted or when fecal microbiota transplantation was administered.