The Urinary Microbiome of Older Adults Residing in a Nursing Home Varies With Duration of Residence and Shows Increases in Potential Pathogens

Abstract

The community of bacteria that colonize the urinary tract, the urinary microbiome, is hypothesized to influence a wide variety of urinary tract conditions. Older adults who reside in nursing homes are frequently diagnosed and treated for urinary tract conditions such as urinary tract infection. We investigated the urinary microbiome of older adults residing in a nursing home to determine if there are features of the urinary microbiome that are associated with specific conditions and exposure in this population. We were also interested in the stability of urinary microbiome over time and in similarities between the urinary and gastrointestinal microbiome. Urine samples were prospectively collected over a period of 10 months from a cohort of 26 older adults (aged >65 years) residing in a single nursing home located in Central Massachusetts. Serial samples were obtained from 6 individuals over 10 months and 5 participants were concurrently enrolled in a study of the gastrointestinal microbiome. Information collected on participants included demographics, medical history, duration of residence in the nursing home, frailty, dementia symptoms, urinary symptoms, antibiotic treatment, urinary catheterization, and hospitalizations over a 10-month period. Clean catch, midstream urine samples were collected and stored at -80°C. DNA was extracted and 16S rRNA gene sequencing was performed. The length of stay in the nursing facility and the Clinical Frailty Scale correlated with significant changes in microbiome composition. An increase in the relative abundance of a putative urinary pathogen, Aerococcus urinae, was the largest factor influencing change that occurred over the duration of residence.

Keywords: Infection; Older adult nursing home residents; Urinary microbiome; Urinary tract infections.

Figure 1.

Bray-Curtis dissimilarity distance between samples plotted by t-distributed stochastic neighbor embedding (tSNE). Numbers associated with individual points denote the study participant that the sample was obtained from. Points are color-coded according to the duration the participant had resided in the nursing home.

Figure 2.

Mixed-effects random forest model of Operational Taxonomic Unit (OTU) abundance associated with duration of residence in the nursing home. Panel A shows the permuted variable importance of the top 10 OTUs that show changes in relative abundance associated with longer duration of residence in the nursing home with the most important contributor being the potential urinary pathogen Aerococcus urinae. Panel B shows the relative abundance of OTUs that show variation associated with duration of residence in the nursing home in the mixed-effect random forest (MERF) model with a significance of p < .1 plotted against time of residence within the nursing home. Each plotted point represents an individual sample. Three organisms, Aerococcus urinae, Dilaster pneumosinties, and Clostridium cluster XIVa, show high importance in the model and are significantly associated with increasing duration of residence in the nursing home.

Figure 3.

Barplots of detected bacterial genera and relative abundance. The numbers above plots denote study participants. Of note, Participants 1, 2, 6, and 7 received courses of antibiotics between the first and second analyzed samples.

Figure 4.

Bray-Curtis dissimilarity distance between samples plotted by t-distributed stochastic neighbor embedding (tSNE) according to the study participant. Numbers associated with individual points denote the individual sample. Points are color-coded according to the participant the sample was obtained from.