Next Generation Sequencing for Microbial Analysis to Select Prophylactic Antibiotic Selection before Urologic Stone Surgery: A Culture Change

Abstract

Background: This paper aims to determine if the combination of polymerase chain reaction (PCR) and next-generation sequencing (NGS) could identify bacteria in culture-negative urine that would alter prophylaxis management. Methods: We sent approximately 5 - 10 mL of a preoperative urine sample to MicrogenDx for PCR/NGS analysis performed after surgery (blind to the surgeon). The physician prescribed standard of care antibiotic prophylaxis. Cases modeling the hospital course of 3 random patients were reviewed by eight urologists after surgery to determine if NGS results would change their prophylaxis regimen. An infectious disease pharmacist reviewed the cases and provided the “ideal” regimen. Results: Urine cultures identified bacteria in 11% (2/18) of cases. Culture speciation results were consistent with NGS results. NGS detected a dominant bacteria in 56% (10/18) of negative cultures and targetable bacteria in all samples. There was a 15% (3/20) infection rate. In both cases, NGS results suggest inadequate prophylaxis. In response to the case scenarios, 100%, 88%, and 88% of the urologists reported they would change prophylaxis with NGS results. During a case scenario, physicians would tend to overprescribe antibiotics given PCR/NGS data for prophylaxis selection. Conclusion: NGS identifies a targetable bacterium in up to 80% of negative urine cultures before urologic stone surgery. Responses to case scenarios indicate that physicians would change management based on NGS results. Inter-professional (urologic and pharmacy) antibiotic selection with PCR/16S DNA testing may be helpful to improve antibiotic stewardship.