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Observational Study
. 2019 Mar;60(2):75-83.
doi: 10.4111/icu.2019.60.2.75. Epub 2019 Feb 27.

Microbiome Diversity in Carriers of Fluoroquinolone Resistant Escherichia coli

Free PMC article
Observational Study

Microbiome Diversity in Carriers of Fluoroquinolone Resistant Escherichia coli

Michael A Liss et al. Investig Clin Urol. .
Free PMC article


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.

Keywords: Anti-bacterial agents; Escherichia coli; Infection; Microbiota; Prostate.

Conflict of interest statement

CONFLICTS OF INTEREST: Resphera Biosciences was paid to perform the microbiome analysis, and Dr. White is the owner of the company.


Fig. 1
Fig. 1. Consort flow diagram. FQR, fluoroquinolone-resistant.
Fig. 2
Fig. 2. Beta diversity principal components analysis.
Fig. 3
Fig. 3. Waterfall plot demonstrating the variability of bacterial taxa associated with or without fluoroquinolone resistant colonization.
Fig. 4
Fig. 4. Correlation analysis map.
Fig. 5
Fig. 5. Differentially abundant taxa associated with resistance status.

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