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

Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry JD, Van der Pol B - PLoS ONE (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of North Texas, Denton, Texas, United States of America.

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.

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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.
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pone-0019709-g002: 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.

Mentions: Because our above analyses considered urine and swab specimens in groups, we also used Kolmogorov-Smirnov (KS) testing to assess the similarity of microbiomes in individual (corresponding) urine swab pairs. Bacterial distributions did not significantly differ in any of the 10 STI positive sample pairs. Of the 22 specimen pairs from STI negative men, only two differed by KS test (subject#15, p = 0.0497, FDR = 54.68%; and subject #26, p = 0.0246, FDR = 54.19%). Separately, hierarchical clustering of all urine and swab specimens was performed using pair-wise Spearman's ranked correlation coefficients. Supporting KS test results, the closest match of most individual urine or swab specimens was usually the corresponding specimen (Figure 2). Interestingly, clustering analysis indicated that the two specimens from subject 15 were more similar to each other than to all other specimens in the group of healthy men (Figure 2). Collectively, these results suggested that first-catch urine and urethral swabs similarly sampled male urethral microbiomes.


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

Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry JD, Van der Pol B - PLoS ONE (2011)

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.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3094389&req=5

pone-0019709-g002: 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.
Mentions: Because our above analyses considered urine and swab specimens in groups, we also used Kolmogorov-Smirnov (KS) testing to assess the similarity of microbiomes in individual (corresponding) urine swab pairs. Bacterial distributions did not significantly differ in any of the 10 STI positive sample pairs. Of the 22 specimen pairs from STI negative men, only two differed by KS test (subject#15, p = 0.0497, FDR = 54.68%; and subject #26, p = 0.0246, FDR = 54.19%). Separately, hierarchical clustering of all urine and swab specimens was performed using pair-wise Spearman's ranked correlation coefficients. Supporting KS test results, the closest match of most individual urine or swab specimens was usually the corresponding specimen (Figure 2). Interestingly, clustering analysis indicated that the two specimens from subject 15 were more similar to each other than to all other specimens in the group of healthy men (Figure 2). Collectively, these results suggested that first-catch urine and urethral swabs similarly sampled male urethral microbiomes.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of North Texas, Denton, Texas, United States of America.

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.

Show MeSH