Comparative Effectiveness Randomized Clinical Trial Using Next-generation Microbial Sequencing to Direct Prophylactic Antibiotic Choice Before Urologic Stone Lithotripsy Using an Interprofessional Model

Abstract

Background: Next-generation sequencing (NGS) methods for microbial profiling have increased sensitivity to detect urinary pathogens.

Objective: To determine whether NGS microbial profiling can be used to guide antibiotic prophylaxis and reduce infection compared with the standard of care.

Design setting and participants: A prospective randomized controlled clinical trial of patients undergoing urologic stone interventions at an academic health center from December 2019 to January 2022 was conducted. Urine was collected at the preoperative visit for standard culture and intervention NGS diagnostics. Evaluable patients were culture negative, met 2-wk follow-up, and did not cancel surgery. Of 240 individuals (control = 121, intervention = 119), 83 control and 74 intervention patients were evaluable.

Intervention: Microbial findings (paired quantitative polymerase chain reaction and NGS) were sent to an infectious disease pharmacist to recommend prophylactic antimicrobial regimen.

Outcome measurements and statistical analysis: The primary outcome was postoperative urinary infection within the follow-up period (Fisher's exact test). The primary outcome was analyzed by modified intent-to-treat (mITT) and per-protocol analyses. Secondary endpoints considered included positive culture concordance, antibiotic use, and adverse events. Additional post hoc analyses investigated factors contributing to infection (univariate logistic regression).

Results and limitations: The intervention significantly reduced postsurgical urinary infection risk by 7.1% (-0.73%, 15%) compared with the standard of care in the mITT analysis (1.4% vs 8.4%, p = 0.045) or by 8.5% (0.88%, 16%) compared with the per-protocol analysis (0% vs 8.5%, p = 0.032). NGS-guided treatment altered the distribution of antibiotics used (p = 0.025), and antibiotics poorly matched with NGS findings were associated with increased infection odds (odds ratio [OR] = 5.9, p = 0.046). Women were at greater odds to develop infection (OR = 10, p = 0.03) and possessed differentiated microbial profiles (p < 0.001).

Conclusions: Urinary microbial NGS-guided antibiotic prophylaxis before endoscopic urologic stone lithotripsy improves antibiotic selection to reduce healthcare-associated urinary infections; however, treatment efficacy may be limited by the ability to adhere to the recommended protocol.

Patient summary: We investigated whether microbial DNA sequencing could improve the selection of antibiotics before kidney stone surgery in patients not known to have any bacteria in the urine on standard culture. We found that using microbe DNA to guide antibiotic choices decreased postoperative infection rate and may encourage individualized use of available antibiotics.

Keywords: Infection; Kidney stone; Lithotripsy; Microbiome; Next-generation sequencing.

© 2023 The Author(s).

Figures

Fig. 1

Graphic consort diagram of randomized clinical trial and modified intent-to-treat analysis. We enrolled 240 patients from a single institution in a phase 2 randomized trial. Patients were randomized at the time of urine collection in the clinic at the time of surgery scheduling. Only those patients who had a negative urine culture were randomized, leading to many cases of exclusion upfront. We report a significant reduction in infections in a modified intent-to-treat analysis using a one-tailed Fischer’s exact test. The differences between groups were compared using a two-sample test for equality of proportions. CI = confidence interval; mITT = modified intent to treat; NGS = next-generation sequencing.

Fig. 2

UpSet plots comparing antibiotic use. The UpSet plots show differential pattern of antibiotic usage between the intervention (left), control as used (middle), and control post hoc antibiotic recommendation (right) comparison sets. Points connected by lines indicate where combination antibiotics were used during treatment. Intersection bar plots show the number of times a specific antibiotic was used alone or in combination with another, whereas the right-hand bar plots show the number of times an antibiotic was used in total.

Fig. 3

Differential microbial profiles by gender at baseline. (A) The total number of species quantified by both qPCR and NGS shown as per patient-reported gender. (B) For patients with NGS-positive 16S rRNA results, bacterial relative abundances were summarized by Bray-Curtis dissimilarity and clustered naively by PCoA; 95% confidence ellipses were added to show group-wise clustering of male versus female baseline measurements. A species-level biplot was added to show the top five species maximally correlated to axes 1 and 2. The arrow length is proportional to correlational strength. (C) Following ANCOM, four species were found to be significantly different in abundance between genders, after multiple test correction (q < 0.05). Error bars indicate standard error around each mean relative abundance. ANOVA = analysis of variance; NGS = next-generation sequencing; PCoA = principal coordinate analysis; qPCR = quantitative polymerase chain reaction.

Fig. 4

Heatmap of trial results. Heatmap shows findings per paired 16S rRNA sequencing and qPCR panel used to guide antibiotic recommendations in culture-negative patients undergoing urologic stone intervention procedures. Infection relates to occurrence of postoperative infections within the follow-up period, documented by visit to emergency room. NGS (positive or negative) relates to the findings by the commercial NGS provider MicroGen DX. Negative samples had no findings by sequencing or qPCR. NGS species are presented as reported in reports to physician and by relative abundance; here, the top 25 bacteria out of 153 total are shown. The qPCR species are shown as log-transformed abundance, with top six of 16 observed here. A prefix of b: versus f: is used to indicate bacterial versus fungal detections. Following are the findings of qPCR assays that report the detection of common antibiotic resistance–associated genes by the class of antibiotic with detected resistance. Antibiotic prophylaxis (ABXProphylaxis) shows the actual antibiotic(s) given per patient, which may differ from recommendations. The AntibioticRecommended row shows antibiotics recommended for the intervention arm by an ID pharmacist. The PostHocRecommendation row shows recommendations for a treating antibiotic made after the study had concluded, to determine how often treatment may have been changed in the control arm. Lastly, the ABXMatch column shows where the actual antibiotic(s) given in the study was consistent with the recommendation column. ABX = antibiotic; ARG = antibiotic resistance gene; ID = infectious disease; NGS = next-generation sequencing; qPCR = quantitative polymerase chain reaction.