The new world of the urinary microbiota in women

Abstract

Emerging evidence challenges the long-held paradigm that the healthy bladder is sterile. These discoveries may provide new opportunities to address important women's health conditions, which include preterm labor and delivery, urinary tract infections, and common forms of urinary incontinence. Traditional tools for urinary bacterial assessment, which includes urinary dipsticks and standard urine cultures, have significant limitations that restrict the information that is available to clinicians. For example, the standard urine culture does not detect slow-growing bacteria that die in the presence of oxygen. Two new, complementary tools, however, can detect these and other organisms, which permits a more complete characterization of bacterial communities within the female bladder. Obstetrician-gynecologists should become familiar with these new approaches (expanded quantitative urine culture and 16S ribosomal RNA gene sequencing) that can detect previously unrecognized organisms. These advances are making it possible to answer previously intractable scientific and clinical questions. Traditional nomenclature used to describe the bacterial status in the bladder is quite dated and unsuited for the emerging information about the bacterial milieu of the female urinary tract. In the context of the sterile bladder paradigm, clinicians have learned about "uropathogens," "asymptomatic bacteriuria," and "urinary tract infection." Given that the lower urinary tract is not sterile, these terms should be reevaluated. Clinicians can already benefit from the emerging knowledge regarding urinary organisms that have previously gone undetected or unappreciated. For example, in some subpopulations of women with urinary symptoms, existing data suggest that the urinary bacterial community may be associated with women's health conditions of interest. This Clinical Opinion highlights the inadequacies of the current tools for urinary bacterial assessment, describes the new assessment tools, explains the current interpretation of the resulting data, and proposes potential clinical uses and relevance. A new world is opening to our view that will give us the opportunity to better understand urinary bacteria and the bladder in which they live. This new knowledge has significant potential to improve patient care in obstetrics and gynecology.

Keywords: 16S rRNA sequencing; asymptomatic bacteriuria; microbiome; microbiota; urgency urinary incontinence; urinary tract infection; urine culture.

Figure 1

Relatedness of each microbiome profile as measured by Bray-Curtis method shown in a dendrogram (top), and by relative abundance of classified sequences as shown in the histogram (bottom). In a dendrogram, the length of each branch represents the relatedness between groups. The more related, the shorter the branch. We can group each branch to determine clusters. The histogram displays the bacterial taxa detected in each sample, as a percent of the total sequence reads classified. Each color represents a different family or genus. By comparing the dendrogram clustering to the classification, we can define urotypes, which are named on the basis of the dominant (most common) classified organism in each sample.

Figure 2

Rarefaction curves of cultured bacterial species by cohort: Women with Urgency Urinary Incontinence versus Women without Urgency Urinary Incontinence. The plot depicts the number of unique species cultured via EQUC by the number of urines assayed.