Urine is not sterile and the urinary tract harbours its distinct microbiota which is different from the genital microbiota. The overall number of bacteria present in urine of healthy patients is regarded as rather low due to the presence of antimicrobial defence mechanisms and unfavourable growth conditions. The risk for urinary tract infections (UTIs); which may lead to pyelonephritis and urosepsis; is potentiated in the presence of medical devices that provide a surface for bacterial biofilm formation.
The biofilm lifestyle may turn normally harmless; commensal bacteria into pathogens and is with increased antimicrobial resistance. The typical encrustations of organic and inorganic, including microbial biofilms formed during 3-6 weeks on ureteral stents in patients treated for kidney and ureteral stones, and without urinary tract infection at the time of stent insertion.
Presence of different urotypes
Next-generation sequencing of the 16S rRNA gene V3-V4 region revealed presence of different urotypes; distinct bacterial communities. Analysis of bacterial load was 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.
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 classified according to different urotypes, some of which dominated by potentially pathogenic species. Facultative pathogens however appear to a common feature in patients without clinically manifested urinary tract infection.
The microbiome of ureteral stent
This work provides insights into the microbiome of ureteral stent encrustations and information on the bacterial contribution to these encrustations for the first time. In contrast to microbiome studies investigating samples of high bacterial content the low bacterial load in urinary tract samples complicates the generation of accurate microbiota profiles. Accordingly, contaminations from reagents or sample processing may mask the signal of resident microbiota. Moreover, PCR-inhibitors and human DNA transrenally excreted to the urine may complicate the detection of bacteria.
Furthermore, it can anticipated that a certain proportion of bacterial DNA detected in urine or the urinary tract derives from extracellular DNA (eDNA) of degraded bacterial cells anywhere in the body; since eDNA is able to pass the kidney barrier in healthy humans. However, the adsorption of eDNA to crystals and polymers may reduce the efficiency of the DNase digestion; as it for example for eDNA adsorbed to graphene oxide.