Concordance of Urobiome Findings in Self-collected Urine: Home vs. Research Site

Thursday, October 24, 2024

12:36 PM – 12:40 PM EDT

Location: Independence Ballroom E-H (Meeting Level 4)

Table 1.docx

Objectives: This sub-study evaluated concordance of self-collected urogenital microbiota at home on 2 consecutive days, and at home vs. a clinical research setting, using advanced contamination controls and ecological metrics.

Methods: A sub-set of community-dwelling women enrolled in the U.S. population-based RISE FOR HEALTH study provided voided urogenital samples at up to three time points: 1) 1-day prior to in-person evaluation; 2) on the day of, prior to in-person evaluation, and 3) during in-person evaluation. Participants collected midstream samples using the Peezy™ device and shipped them to a central laboratory.1 Samples participants were sequenced with V4 16S rRNA gene amplicon sequencing with Earth Microbiome Project protocols for bacterial DNA. KatharoSeq removed samples where sequences were indistinguishable from background. Data was matched to Greengenes2-2022.10 and rarefied to 1000 seqs/sample for microbial ecology analyses. Unweighted UniFrac distances, Mantel Pearson correlations and Kruskal Wallis tests were used for comparisons. Chi-squared tests evaluated concordance across time points. Inter-sample concordance between time points was determined in individuals with sample pairs that were above the KatharoSeq threshold, either using two home samples or one home and one research site sample.

Results: Detectable sequences were obtained in 261 samples from the 114 participants and 187 (72%) were above the KatharoSeq threshold. Table 1 lists the most prevalent genera. Inter-sample concordance between two time points was determined for samples above the threshold from 38 participants with two home samples and 47 between one home and one clinic sample. We observed no significant difference in concordance by timepoint (X2=2.72, p=0.256). Mantel correlations between two home collection time points were significant (Fig1A, r=0.43, p=0.001). Because home specimens were similar, an arbitrary single home sample was compared with clinic collection. Significant positive Mantel correlations were noted between home and clinic (Fig1C, r=0.362, p=0.001). Samples from the same participant were more similar to each other than to any sample from other participants when comparing the two home collections (Fig1B) or home and clinic collections (Fig1D).

Conclusions: Home-collected urine samples for urogenital microbiome ecological analysis have sufficient short-term similarity and concordance with self-collected urine samples from a research clinic setting for subsequent ecological analyses. The variability observed within and between individuals is consistent with expected variation of urobiome samples.2 Multiple variables can affect variability of urine samples between and within individuals over time due to factors including diet, hydration, and underlying health conditions.3 Stringent filtering to reduce erroneous taxon detection from reagents and conservative estimates of community characteristics are essential for rigorous interpretation of this low biomass fluid. These findings are comparable with cross-timepoint correlations within microbiome datasets used for biological patterns at other body sites.4 Additional work is needed to develop cost-effective sequencing techniques for use in population-based urobiome research.

Disclosure(s):

Emily Lukacz, MD: No relevant disclosure to display

Daniel McDonald, PhD: BiomeSense, Inc: Consultant/Advisory Board (Ongoing), Stock-privately held company (Ongoing)

MacKenzie Bryant, MS: No financial relationships to disclose

Sara Putnam, MS: No financial relationships to disclose

Kyle Rudser, PhD: No financial relationships to disclose

Caitriona Brennan, BSc: No financial relationships to disclose

Melanie R. Meister, MD, MSCI: No relevant disclosure to display

Cora E. Lewis, MD: No financial relationships to disclose

Cynthia S. Fok, MD MPH: No relevant disclosure to display

Margaret Mueller, MD: No relevant disclosure to display

Rob Knight, PhD: No relevant disclosure to display

Linda Brubaker, Co-Author: No relevant disclosure to display

Presenting Author(s)

Emily Lukacz, MD

Professor, Division Director Urogynecology
University of California San Diego
La Jolla, California, United States

Disclosure(s): No relevant disclosure to display

Co-Author(s)

DM

Daniel McDonald, PhD (he/him/his)

Scientific Director, The Microsetta Initiative
UC San Diego School of Medicine
La Jolla, California, United States

Disclosure(s): BiomeSense, Inc: Consultant/Advisory Board (Ongoing), Stock-privately held company (Ongoing)
MB

MacKenzie Bryant, MS

Research Data Analyst
University of California San Diego
Raleigh, North Carolina, United States

Disclosure(s): No financial relationships to disclose
SP

Sara Putnam, MS (she/her/hers)

Systems and Database Administrator
University of Minnesota
Greenville, South Carolina, United States

Disclosure(s): No financial relationships to disclose
KR

Kyle Rudser, PhD

Professor of Biostatistics
University of Minnesota
Minneapolis, Minnesota, United States

Disclosure(s): No financial relationships to disclose
CB

Caitriona Brennan, BSc

PhD Student
University of California San Diego
San Diego, California, United States

Disclosure(s): No financial relationships to disclose
Melanie R. Meister, MD, MSCI (she/her/hers)

Associate Professor
University of Kansas
Overland Park, Kansas, United States

Disclosure(s): No relevant disclosure to display
CL

Cora E. Lewis, MD

Chair, Dept. Of Epidemiology
University of Alabama at Birmingham
Birmingham, Alabama, United States

Disclosure(s): No financial relationships to disclose
CF

Cynthia S. Fok, MD MPH (she/her/hers)

Associate Professor Department of Urology
University of Minnesota
Minneapolis, Minnesota, United States

Disclosure(s): No relevant disclosure to display
MM

Margaret Mueller, MD

Associate Professor
University of Chicago Medicine
Glencoe, Illinois, United States

Disclosure(s): No relevant disclosure to display
RK

Rob Knight, PhD

Professor
University of California San Diego
La Jolla, California, United States

Disclosure(s): No relevant disclosure to display
LB

Linda Brubaker, Co-Author

Physician
UC San Diego
Rancho Santa Fe, California, United States

Disclosure(s): No relevant disclosure to display