Investig Clin Urol.  2019 Mar;60(2):75-83. 10.4111/icu.2019.60.2.75.

Microbiome diversity in carriers of fluoroquinolone resistant Escherichia coli

• Liss MA
• Leach RJ
• Rourke E
• Sherrill A
• Johnson-Pais T
• Lai Z
• Basler J
• White JR
• Patterson

• KMID: 2438817
• DOI: http://doi.org/10.4111/icu.2019.60.2.75

Abstract

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.

Keyword

Anti-bacterial agents; Escherichia coli; Infection; Microbiota; Prostate

MeSH Terms

Agar
Anti-Bacterial Agents
Bacteria
Biopsy
Ciprofloxacin
Colon
Enterobacteriaceae
Escherichia coli*
Escherichia*
Humans
Male
Microbiota*
Observational Study
Prevotella
Prostate
Standard of Care
Agar
Anti-Bacterial Agents
Ciprofloxacin

Figure

• 

  Fig. 1 Consort flow diagram. FQR, fluoroquinolone-resistant.

• 

  Fig. 2 Beta diversity principal components analysis.

• 

  Fig. 3 Waterfall plot demonstrating the variability of bacterial taxa associated with or without fluoroquinolone resistant colonization.

• 

  Fig. 4 Correlation analysis map.

• 

  Fig. 5 Differentially abundant taxa associated with resistance status.

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