Ureteral Stent Microbiota Is Associated with Patient Comorbidities but Not Antibiotic Exposure

Abstract

Ureteral stents are commonly used to prevent urinary obstruction but can become colonized by bacteria and encrusted, leading to clinical complications. Despite recent discovery and characterization of the healthy urinary microbiota, stent-associated bacteria and their impact on encrustation are largely underexplored. We profile the microbiota of patients with typical short-term stents, as well as over 30 atypical cases (all with paired mid-stream urine) from 241 patients. Indwelling time, age, and various patient comorbidities correlate with alterations to the stent microbiota composition, whereas antibiotic exposure, urinary tract infection (UTI), and stent placement method do not. The stent microbiota most likely originates from adhesion of resident urinary microbes but subsequently diverges to a distinct, reproducible population, thereby negating the urine as a biomarker for stent encrustation or microbiota. Urological practice should reconsider standalone prophylactic antibiotics in favor of tailored therapies based on patient comorbidities in efforts to minimize bacterial burden, encrustation, and complications of ureteral stents.

Keywords: antibiotics; endourology; medical microbiology; microbiota; ureteral stents; urology.

Graphical abstract

Figure 1

The Stent Microbiota Is Dominated by Urinary Bacteria Samples are plotted left to right and ordered by the dendrogram. The dendrogram was generated from CLR-transformed read counts grouped by genera, based on the average linkage clustering of per-sample Aitchison distance. Branches of the dendrogram are colored by sample type (stents are navy; urine is orange). The heatmap represents the relative abundance of genera within samples (more abundant genera are lighter in color). Color coding below the heatmap corresponds to patient gender (females are pink; males are blue). An excerpt from the fourteen leftmost branches of the tree illustrates that, in general, samples from the same individual group nearby on the dendrogram (see also Figure S4A). n = 667; 213 urine and 454 stent samples from 241 patients.

Figure 2

Principal-Component Analysis of Longitudinal Samples (A) PCA was performed on CLR-transformed Aitchison distances of longitudinally collected samples. Each colored point represents a sample. Distance between samples on the plot represents differences in microbial community composition, with 24.9% of total variance being explained by the first two components shown. Strength and association for genera (sequence variants) are depicted by the length and direction of the gray arrows, respectively. Points are colored by participant and shaped by visit number. n = 64. (B) Aitchison distance was greater between interindividual samples of the same type (n = 1,254) than between samples from the same participant of the same type at different visits (n = 37; Bonferroni-corrected Mann-Whitney U test; p < 0.0001). Boxplot whiskers represent minimum and maximum. (C) Representative relative abundance bar plot of three longitudinal stent patients. Each vertical bar represents the relative SV abundance within a single sample. Samples are grouped by participant. Relative abundance of SVs is colored by genera, with common genera shown in the legend. Days between sample collections are listed in the green visit code.

Figure 3

Microbial Communities of Bilateral Stents (A) PCA was performed on CLR-transformed Aitchison distances of samples from patients with bilateral indwelling stents. Each colored point represents a sample. Distance between samples on the plot represents differences in microbial community composition, with 29.3% of total variance being explained by the first two components shown. Strength and association for genera (sequence variants) are depicted by the length and direction of the gray arrows, respectively. Points are colored by participant and shaped by sample type, which include both proximal and distal stent ends (n = 55). (B) Aitchison distance was compared between interindividual samples and intraindividual samples. S, distance between stent samples from the same participant (n = 154); U versus S, distance between urine and stent samples from the same participant (n = 39); all, all samples from a single participant (n = 234). All intraindividual comparisons had significantly shorter distances than the distance between samples from different individuals (n = 2,736; Bonferroni-corrected Dunn’s tests; p < 0.0001). In intraindividual comparisons, the distance was shortest between stent samples and furthest from urine to stent samples (p = 0.022). Boxplot whiskers represent minimum and maximum. (C) Representative relative abundance bar plot of three bilateral stent patients. Each vertical bar represents the relative SV abundance within a single sample. Samples are grouped by participant. Relative abundance of SVs is colored by genera, with common genera shown in the legend. Sample type is color coded. Stents from the left side are denoted by “L” and from the right side by “R”; urine is denoted by “U.”

Figure 4

Stent Microbiota and Encrustation Are Unchanged by Antibiotic Exposure, Device Placement Method, and UTI PCA was performed on CLR-transformed Aitchison distances. Each colored point represents a sample. Distance between samples on the plot represents differences in microbial community composition, with 20.5% of total variance being explained by the first two components shown. Strength and association for genera (sequence variants) are depicted by the length and direction of the gray arrows, respectively. (A, D, and G) Samples are colored based on (A) whether the study participant had exposure to antibiotics within the last 30 days prior to sample collection (blue) or not (pink), (D) whether the stents were placed in a retrograde (purple) or antegrade (orange) manner, and (G) whether the participant had a UTI within 7 days of stent placement or throughout the indwelling period (orange) or not (green). Ellipses represent the 95% confidence interval. (B, E, and H) The degree of stent encrustation was compared between groups of interest. Groups were not significantly different by two-tailed Mann-Whitney U test. (C, F, and I) Shannon’s index of alpha diversity was not significantly different between antibiotic (C) or placement (F) groups, but patients with a UTI had lower diversity than those without (I; two-tailed Mann-Whitney U test; p = 0.002). Boxplot whiskers represent minimum and maximum.

Figure 5

SEM Confirms the Presence of Urinary Crystals and Bacterial Biofilms Representative scanning electron micrographs of stent encrustations illustrating typical bacterial biofilms and crystal morphologies. Based on microbiota sequencing, bacteria visible (white arrowheads) likely correspond to the genera (014) Lactobacillus and (195) Enterococcus. X-ray diffraction of crystalline microstructures (white arrows) correspond to calcium oxalate dihydrate (010 and 019a), calcium oxalate monohydrate in oval (022) and multiple-twinning (095) morphologies, and calcium phosphate (019b and 195). Scale bars represent 20 μm.