Microbiome diversity in carriers of fluoroquinolone resistant Escherichia coli

• Published in: Investigative and clinical urology Vol. 60; no. 2; pp. 75 - 83
• Main Authors: Liss, Michael A, Leach, Robin J, Rourke, Elizabeth, Sherrill, Allison, Johnson-Pais, Teresa, Lai, Zhao, Basler, Joseph, White, James R, Patterson, Jan E
• Format: Journal Article
• Language: English
• Published: Korea (South) The Korean Urological Association 01.03.2019; Korean Urological Association; 대한비뇨의학회
• Subjects: Aged; Anti-bacterial agents; Carrier State; Drug Resistance, Bacterial; Escherichia coli; Escherichia coli - drug effects; Escherichia coli - isolation & purification; Escherichia coli Infections - microbiology; Fluoroquinolones - pharmacology; Gastrointestinal Microbiome; Humans; Infection; Male; Microbiota; Middle Aged; Original; Prostate; Rectum - microbiology; 비뇨기과학; Infection; Microbiota; Anti-bacterial agents; Prostate; Escherichia coli
• DOI: 10.4111/icu.2019.60.2.75
• ISSN: 2466-0493

Fluoroquinolone-resistant (FQR) 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. 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. 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). Microbiome analysis determined that men colonized with FQR bacteria have less diverse bacterial communities (dysbiosis), higher levels of Enterobacteriaceae and reduced levels of . These results may have implications in pre/probiotic intervention studies.