The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens

Abstract

Urine is the CDC-recommended specimen for STI testing. It was unknown if the bacterial communities (microbiomes) in urine reflected those in the distal male urethra. We compared microbiomes of 32 paired urine and urethral swab specimens obtained from adult men attending an STD clinic, by 16S rRNA PCR and deep pyrosequencing. Microbiomes of urine and swabs were remarkably similar, regardless of STI status of the subjects. Thus, urine can be used to characterize urethral microbiomes when swabs are undesirable, such as in population-based studies of the urethral microbiome or where multiple sampling of participants is required.

Figure 1. The proportions of bacterial genera in urine and swab specimens are similar.

The y-axis shows percentage classified sequence reads corresponding to each genera, bars corresponding to urine and swab are in gray and black, respectively. Error bars indicate one unit of standard error. The 15 most abundant genera, corresponding to 89.48% and 83.52% of classifiable sequences from STI positive and negative specimens, respectively, are shown. (A). STI (positive test for C. trachomatis, N. gonorrhoeae, and or T. vaginalis) positive group (n = 10), (B) STI negative group (n = 22).

Figure 2. Hierarchical clustering sorts specimens into urine swab pairs.

Spearman's rank correlation coefficients were calculated using relative abundance of the 20 most abundant genera in each specimen, which account for 90.91% and 86.39% of classifiable sequences in swabs and urines, respectively. Yellow indicates urine, purple indicates swab specimen. The color gradient indicates relative abundance of the genera in each specimen (red for most abundant bacteria). (A). STI positive group (n = 10). (B) STI negative group (n = 22). Note that most swab and urine specimens from individual subjects cluster together.