Prospective Implementation of a Point-of-Care PCR-Based Detection Method to Guide Antibiotic Use Prior to Prostate Biopsy Compared to Targeted Prophylaxis and Physician Choice.

OBJECTIVE: To perform pilot testing regarding implementation of a point-of-care qPCR-based test (EST200) targeting bacterial clonal groups representing the majority of sepsis-causing Escherichia coli before prostate biopsy to determine antibiotic selection. MATERIALS AND METHODS: After IRB approval, we obtained rectal swabs to compare real-time qPCR analysis on a Rotor-Gene Q instrument (Qiagen, Hilden, Germany) to standard culture on ciprofloxacin infused (10mg/L) MacConkey agar and susceptibility testing. Techniques are compared by an area under the receiver operative curve (AUC). RESULTS: A total of 140 men participated in the study, 102 prebiopsy cultures were utilized to guide prophylaxis. We did not meet our accrual for the randomized portion of the clinical study, yet we did randomized 38 men without prebiopsy cultures to physician choice of antibiotic versus PCR-based approach. Regarding predicting Fluoroquinolone Resistant (FQR) at biopsy, prebiopsy cultures had an AUC of 0.91 (95%CI 0.84-1.00, P > .001) and polymerase chain reaction (PCR) had an AUC of 0.71 (95%CI 0.58-0.84, P = .005) (AUC comparison; Z = 2.31, P = .02). PCR correctly identified 4 of 5 FQR specimens. The PCR test attained an AUC of 0.79 (95%CI 0.56-1.00, P = .044) for detection of total FQR on the day of the biopsy. Risk-based techniques may overcompensate with additional antibiotics (21% versus 0%, P = .10). CONCLUSION: EST200 is a rapid PCR-based microbial detection system that has moderate ability to detect total FQR at the time of biopsy. Our study is underpowered, yet provide opportunities to improve the point of care PCR method, such as table tope testing in less than 20 minutes and include additional antibacterial resistant genes.

Microbiome diversity in carriers of fluoroquinolone resistant Escherichia coli.

Purpose: Fluoroquinolone-resistant (FQR) Escherichia coli causes transrectal prostate biopsy infections. In order to reduce colonization of these bacteria in carriers, we would like to understand the surrounding microbiome to determine targets for decolonization. Materials and Methods: We perform an observational study to investigate the microbiome differences in men with and without FQR organisms found on rectal culture. A rectal swab with two culturettes was performed on men before an upcoming prostate biopsy procedure as standard of care to perform "targeted prophylaxis." Detection of FQR was performed by the standard microbiology lab inoculates the swab onto MacConkey agar containing ciprofloxacin. The extra swab was sent for 16S rRNA amplicon sequencing (MiSeq paired-end) using the V1V2 primer. Alpha and beta-diversity analysis were performed using QIIME. We used PERMANOVA to evaluate the statistical significance of beta-diversity distances within and between groups of interest. Results: We collected 116 rectal swab samples before biopsy for 16S rRNA amplicon sequencing. We identified 18 isolates (15.5%, 18/116) that were positive and had relative reduced diversity profiles (p<0.05). Enterobacteriaceae were significantly over-represented in the FQR subjects (adjusted p=0.03). Conclusions: Microbiome analysis determined that men colonized with FQR bacteria have less diverse bacterial communities (dysbiosis), higher levels of Enterobacteriaceae and reduced levels of Prevotella disiens. These results may have implications in pre/probiotic intervention studies.