Randomized clinical trial using next generation microbial sequencing to direct antibiotic selection before kidney stone lithotripsy using an interprofessional model

We conducted a prospective randomized controlled clinical trial of patients undergoing kidney stone interventions at an academic health center from December 2019 to January 2022. Patients were randomized to standard of care or intervention at enrollment. Urine was collected at the time of pre-operative culture collection and aliquoted to standard culture and NGS tubes. For those in the intervention arm with a negative culture, the NGS report was sent to an infectious disease pharmacist to determine the prophylactic antimicrobial regimen. The primary outcome was post-operative urinary infection within 2 weeks of surgery.