Encrustations on ureteral stents from patients without urinary tract infection reveal distinct urotypes and a low bacterial load

Abstract

Background Current knowledge of the urinary tract microbiome is limited to urine analysis and analysis of biofilms formed on Foley catheters. Bacterial biofilms on ureteral stents have rarely been investigated, and no cultivation-independent data are available on the microbiome of the encrustations on the stents. Results The typical encrustations of organic and inorganic urine-derived material, including microbial biofilms formed during 3–6 weeks on ureteral stents in patients treated for kidney and ureteral stones, and without reported urinary tract infection at the time of stent insertion, were analysed. Next-generation sequencing of the 16S rRNA gene V3–V4 region revealed presence of different urotypes, distinct bacterial communities. Analysis of bacterial load was performed by combining quantification of 16S rRNA gene copy numbers by qPCR with microscopy and cultivation-dependent analysis methods, which revealed that ureteral stent biofilms mostly contain low numbers of bacteria. Fluorescence microscopy indicates the presence of extracellular DNA. Bacteria identified in biofilms by microscopy had mostly morphogenic similarities to gram-positive bacteria, in few cases to Lactobacillus and Corynebacterium , while sequencing showed many additional bacterial genera. Weddellite crystals were absent in biofilms of patients with Enterobacterales and Corynebacterium- dominated microbiomes. Conclusions This study provides novel insights into the bacterial burden in ureteral stent encrustations and the urinary tract microbiome. Short-term (3–6 weeks) ureteral stenting is associated with a low load of viable and visible bacteria in ureteral stent encrustations, which may be different from long-term stenting. Patients could be classified according to different urotypes, some of which were dominated by potentially pathogenic species . Facultative pathogens however appear to be a common feature in patients without clinically manifested urinary tract infection. Trial registration ClinicalTrials.gov, NCT02845726 . Registered on 30 June 2016—retrospectively registered. Electronic supplementary material The online version of this article (10.1186/s40168-019-0674-x) contains supplementary material, which is available to authorized users.

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

“… 59 , 60 In future studies, quantification of total 16S rRNA gene copies by qPCR or the use of extended quantitative urine culture may complement and validate microbiota analysis of urinary and ureteral stent samples. 28 , 52 Nevertheless, the detection of reproducible, patient-specific, stent microbiota signatures provides confidence that our findings are not due to contamination.…”

Surface analysis of ureteral stent before and after implantation in the bodies of child patients

“…2) confirmed the encrustations and biofilm formation after post-URS-L implantation for 7 days. SEM imaging indicated thick crystal-containing layers in distal section of the DJ stents, confirmed in the literature as the weddellite, frequently in a tetragonal dipyramidal shape (calcium oxalate dihydrate, CaC 2 O 4 ⋅ 2H 2 O ) [33]. Moreover, the side hole located in the distal section of the DJ stents was completely filled by calcium oxalate film.…”

Actinotignum schaalii: Relation to Concomitants and Connection to Patients’ Conditions in Polymicrobial Biofilms of Urinary Tract Catheters and Urines

“…Since the species richness was higher in UC with both approaches (presence/absence-based PCR-DGGE-S combined with culture, as well as abundance-based NGS), as expected (see Figure 2 , Supplementary Figures S4–S7 ), we do not assume any underestimation in UCs’ species richness. This finding can refer to A. schaalii ’s ability to be present in any catheters’ biofilm (including nephrostomy) [ 2 , 9 , 12 , 18 , 22 , 37 ], regardless of the catheter type. To confirm this hypothesis in non-infected but colonized patients, the cohort with non-catheterized individuals should be examined, although the case series and clinical observations have already defined unspecified catheterization as a risk factor for A. schaalii infection [ 6 , 9 , 12 , 19 , 34 , 35 ].…”

“…Few reports alerting this species’ potential importance in urinary tract polymicrobial communities and its role in catheter biofilms have appeared to date [ 27 , 36 , 37 ]. None of them were focused on urinary and ureteral (double-J) catheters, although A. schaalii had already been reported in both these materials [ 12 , 18 , 22 , 37 ]. Thus, we present observational study focused on A. schaalii on urinary (UC) and ureteral (DJC) catheters.…”