<span class="paragraphSection"><strong>Background:</strong> Recipients of faecal microbiota transplantation (FMT) in treatment of recurrent <span style="font-style:italic;">Clostridium difficile</span> infection (RCDI) remain at markedly increased risk of re-infection with <span style="font-style:italic;">C. difficile</span> with new antibiotic provocations. Urinary tract infections (UTIs) are common indications for antibiotics in these patients, often resulting in <span style="font-style:italic;">C. difficile</span> re-infection.<strong>Methods:</strong> We present a case series of 19 patients treated with parenteral aminoglycosides for UTI following FMT for RCDI. A 3 day outpatient regimen of once-daily intramuscular administration of gentamicin was used to treat 18 consecutive FMT recipients with uncomplicated UTI. One other patient was treated for a complicated UTI with intravenous amikacin. Profiling of 16S rRNA genes was used to track changes in faecal microbial community structure during this regimen in three patients.<strong>Results:</strong> The protocol was highly effective in treating UTI symptoms. None of the patients suffered a re-infection with <span style="font-style:italic;">C. difficile</span>. The faecal microbial communities remained undisturbed by treatment with intramuscular administration of gentamicin.<strong>Conclusions:</strong> Despite falling out of favour in recent years, aminoglycoside antibiotics given parenterally have the advantage of minimal penetration into the gut lumen. A brief (3 day) course of parenteral gentamicin was safe and effective in curing UTI in patients at high risk of <span style="font-style:italic;">C. difficile</span> infection without perturbing their gut microbiota.</span>
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