We monitored the modifications of oral and intestinal microfloras of 10 allogeneic bone marrow recipients who received randomly either norfloxacin or pefloxacin (400 mg three times a day) as selective decontamination for infection prevention. After 1 week of treatment, in all patients members of the family Enterobacteriaceae were no longer detectable and in all but one pefloxacin-treated patient enterococci were also eliminated in the intestine. The anaerobic flora was not affected, with the exception of Bacteroides spp., markedly reduced after treatment with pefloxacin. In most patients the most striking effect was the increase in staphylococcal counts. These strains were found to be resistant to both quinolones in the study. Less consistent changes were observed in oral flora. No relevant difference could be demonstrated between the two regimens on bacterial counts either in feces or in saliva. This study shows the efficacy of both quinolones in eradicating gram-negative bacilli in the alimentary tract of bone marrow transplant patients; however, the finding of the overgrowth of resistant gram-positive organisms during treatment with these agents deserves further evaluation.Infection is the most frequent complication and a major cause of death in patients with profound and prolonged granulocytopenia (11). The principle of selective decontamination of the gastrointestinal tract has been applied successfully to reduce endogenous infection in severely immunocompromised patients: oral antibiotics are used to eliminate the aerobic potentially pathogenic gram-negative organisms in the intestine while preserving the normally predominant anaerobic flora (2,7,8,16,24).Fluoroquinolones, a new class of antibiotics (9, 23) highly active against aerobic gram-negative bacilli, are currently being tested as selective prophylactic regimens during neutropenia. Studies with norfloxacin have been carried out and have demonstrated its efficacy in eliminating gram-negative rods from the intestine of treated patients while sparing the other components of the microflora; this effect was reflected by a decrease in the morbidity associated with gram-negative infections (12, 21). Pefloxacin, one of the newer fluoroquinolones, has a better systemic absorption compared with norfloxacin (22) and could have a prophylactic effect also against bacterial infections originating outside the gastrointestinal tract (e.g., the oral cavity); furthermore, because of the broader spectrum of activity of pefloxacin (3), it might also be a better agent for preventing infections caused by gram-positive organisms.Therefore, we carried out a comparative microbiological study with a group of severely immunocompromised patients as allogeneic bone marrow recipients who received either norfloxacin or pefloxacin as antibiotic prophylaxis. We evaluated the efficacy of the two quinolones in decontaminating the alimentary tract by monitoring the modifications of oral and intestinal microfloras and the emergence of resistant strains.(This work was presented in part...