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. 2023 Jun 7:14:1187625.
doi: 10.3389/fmicb.2023.1187625. eCollection 2023.

Differences in the composition of the bacterial element of the urinary tract microbiome in patients undergoing dialysis and patients after kidney transplantation

Marcelina M Jaworska  1 , Paulina Pecyna  1 , Katarzyna Jaskiewicz  2 , Małgorzata Rydzanicz  3 , Malgorzata Kaluzna  4 , Krzysztof Pawlaczyk  5 , Rafal Ploski  3 , Dorota M Nowak-Malczewska  1 , Justyna A Karolak  1 , Marzena Gajecka  1   2
Affiliations

Differences in the composition of the bacterial element of the urinary tract microbiome in patients undergoing dialysis and patients after kidney transplantation

Marcelina M Jaworska et al. Front Microbiol. .

Abstract

Introduction: The development of molecular biology methods and their application in microbial research allowed the detection of many new pathogens that cause urinary tract infections (UTIs). Despite the advances of using new research techniques, the etiopathogenesis of UTIs, especially in patients undergoing dialysis and patients after kidney transplantation, is still not fully understood.

Methods: This study aimed to characterize and compare the composition of the bacterial element of the urinary tract microbiome between the groups of patients undergoing dialysis (n = 50) and patients after kidney transplantation (n = 50), with positive or negative urine culture, compared to healthy individuals (n = 50).

Results: Asymptomatic bacteriuria was observed in 30% of the urine cultures of patients undergoing dialysis and patients after kidney transplantation, with Escherichia coli as the most dominant microorganism (73%) detected with the use of classical microbiology techniques. However, differences in the bacterial composition of the urine samples between the evaluated patient groups were demonstrated using the amplicon sequencing. Finegoldia, Leptotrichia, and Corynebacterium were found to be discriminative bacteria genera in patients after dialysis and kidney transplantation compared to the control group. In addition, in all of urine samples, including those without bacteriuria in classical urine culture, many types of bacteria have been identified using 16S rRNA sequencing.

Discussion: The revealed microbial characteristics may form the basis in searching for new diagnostic markers in treatment of patients undergoing dialysis and patients after kidney transplantation.

Keywords: dialysis; renal transplantation; urinary tract infection; urine culture; urobiome.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Differences in the composition of the bacterial element of urinary tract microbiome between patients undergoing dialysis (D), patients after renal transplantation (T), and control individuals (C). Identified genera (black triangles) of the bacterial element of the urinary tract microbiome varies between patients undergoing dialysis (blue circle), patients after kidney transplantation (green circle), and control individuals (red circle). Increased abundance in (D) vs. (C) were found for Corynebacterium, Moryella, Finegoldia, and Gallicola. Ochrobactrum was identified more often in (C) comparing to (D). Mogibacterium and Sphingomonas were more often identified in (T) comparing to (C). Propionicimonas was identified with a higher abundance in (C) compared to (T). Increased abundance of genera Moryella, Shuttleworthia, Finegoldia, Gallicola, and Propionigenium was recognized in (D) and Ochrobactrum and Sphingomonas were detected with higher abundance in (T) compared to (D).
Figure 2
Figure 2
α-Diversity of the urinary tract microbiome bacterial element among patients after transplantation, undergoing dialysis, and control individuals. Compared to control samples, the most diverse was the urine microbiota composition among patients undergoing dialysis.
Figure 3
Figure 3
Beta-diversity assessed by the Bray–Curtis dissimilarity tests between patients undergoing dialysis (blue dots), patients after kidney transplantation (green dots), and controls (red dots) based on ASVs. The bacterial element of urine microbiota of patients undergoing dialysis was more variable in composition of microorganisms.
Figure 4
Figure 4
Schematic representation of the bacterial element of the urinary tract microbiome identified in the urine samples of patients and control individuals with positive and negative urine cultures. Blue arrow—dialysis patients, green arrow—patients after kidney transplantation, red arrow—controls; green triangles—names of identified bacteria genera of the bacterial element of the urinary tract microbiome that were found to be discriminative in the studied groups of patients.
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