eThe use of oral vancomycin or metronidazole for treatment of Clostridium difficile infection (CDI) may promote colonization by health care-associated pathogens due to disruption of the intestinal microbiota. Because the macrocyclic antibiotic fidaxomicin causes less alteration of the intestinal microbiota than vancomycin, we hypothesized that it would not lead to a loss of colonization resistance to vancomycin-resistant enterococci (VRE) and extended-spectrum--lactamase-producing Klebsiella pneumoniae (ESBL-Kp). Mice (8 per group) received orogastric saline, vancomycin, or fidaxomicin daily for 5 days at doses resulting in stool concentrations in mice similar to those measured in humans. The mice were challenged with 10 5 CFU of orogastric VRE or ESBL-Kp on day 2 of treatment and concentrations of the pathogens in stool were monitored. The impact of drug exposure on the microbiome was measured by cultures, real-time PCR for selected anaerobic bacteria, and deep sequencing. In comparison to saline controls, oral vancomycin promoted establishment of high-density colonization by VRE and ESBL-Kp in stool (8 to 10 log 10 CFU/g; P < 0.001), whereas fidaxomicin did not (<4 log 10 CFU; P > 0.5). Vancomycin treatment resulted in significant reductions in enterococci, Bacteroides spp., and Clostridium leptum, whereas the population of aerobic and facultative Gramnegative bacilli increased; deep-sequencing analysis demonstrated suppression of Firmicutes and expansion of Proteobacteria during vancomycin treatment. Fidaxomicin did not cause significant alteration of the microbiota. In summary, in contrast to vancomycin, fidaxomicin treatment caused minimal disruption of the intestinal microbiota and did not render the microbiota susceptible to VRE and ESBL-Kp colonization.O ral vancomycin and oral metronidazole are the most commonly used antibiotics for treatment of Clostridium difficile infection (CDI). One limitation of these agents is that they are nonselective (i.e., they inhibit normal anaerobic intestinal microbiota in addition to C. difficile) (1-4). For example, oral vancomycin treatment may result in suppression of Bacteroides/Prevotella, Clostridium coccoides, and Clostridium leptum group organisms in stool (2, 3). Inhibition of the anaerobic microbiota by vancomycin and metronidazole during CDI treatment may contribute to recurrences of CDI and to colonization by health care-associated pathogens such as vancomycin-resistant enterococci (VRE) (4, 5).Fidaxomicin is a macrocycle antibiotic approved by the Food and Drug Administration for the treatment of CDI (1). In comparison to vancomycin, fidaxomicin causes minimal disruption of the anaerobic microbiota and in clinical studies was associated with fewer recurrences of CDI and less frequent acquisition of VRE and Candida spp. during CDI treatment (1, 6). Given the relative sparing of the microbiota during fidaxomicin treatment, we hypothesized that this agent would not lead to a loss of colonization resistance to VRE and extended-spectrum--lactamaseproducing Kleb...