Abstract
Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n = 35) and expanded quantitative urine culture (EQUC, n = 31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.
Highlights
Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection
expanded quantitative urinary culture (EQUC) and next-generation sequencing (NGS) were performed on urine samples from 31 and 35 subjects, respectively
Out of 77 EQUCdetected isolates in these 54 samples, 61 microorganisms (79%) were detectable by NGS. This is the only study to date dedicated to the investigation of the potential differences among first-catch urine (FCU), mid-stream voided urine (MSU) and catheterised urine in men
Summary
Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao[1] and abundance-based coverage estimators. According to a study from 2011, Lactobacillus, Sneathia, Veillonella, Corynebacterium and Prevotella were the abundant bacterial genera detected in male first-catch urine (FCU) as well as urethral swab specimens[4]. Differences in beta- (but not alpha-) diversity were reported in a study of urinary bladder cancer patients between voided and cystoscopy-obtained urine samples[10]. Women with intersticial cystitis/painful bladder syndrome had less diverse microbiota than c ontrols[19]
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