A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples

Vaginitis is a widespread issue for women worldwide, yet current diagnostic tools are lacking. Bacterial vaginosis (BV) is the most prevalent type of vaginitis, found in 10-50% of reproductive-aged women. Current diagnostic methods for BV rely on clinical criteria, microscopy, or the detection of a...

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Bibliographic Details
Published in:Diagnostics (Basel) 2024-09, Vol.14 (18), p.2039
Main Authors: Thomas-White, Krystal, Hilt, Evann E, Olmschenk, Genevieve, Gong, Maryann, Phillips, Caleb D, Jarvis, Courtney, Sanford, Nicholas, White, Jennifer, Navarro, Pita
Format: Article
Language:English
Subjects:
Automation
Bacteria
Brief Report
Classification
Genomes
Health aspects
Infection
Infections
Medical laboratories
Microorganisms
Microscopy
Organisms
Reproducibility
shotgun metagenomic sequencing
Vagina
vaginal microbiome
vaginitis
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Summary:Vaginitis is a widespread issue for women worldwide, yet current diagnostic tools are lacking. Bacterial vaginosis (BV) is the most prevalent type of vaginitis, found in 10-50% of reproductive-aged women. Current diagnostic methods for BV rely on clinical criteria, microscopy, or the detection of a few microbes by qPCR. However, many vaginal infections lack a single etiological agent and are characterized by changes in the vaginal microbiome community structure (e.g., BV is defined as a loss of protective lactobacilli resulting in an overgrowth of anaerobic bacteria). Shotgun metagenomic sequencing provides a comprehensive view of all the organisms present in the vaginal microbiome (VMB), allowing for a better understanding of all potential etiologies. Here, we describe a robust VMB metagenomics sequencing test with a sensitivity of 93.1%, a specificity of 90%, a negative predictive value of 93.4%, and a positive predictive value of 89.6% certified by Clinical Laboratory Improvement Amendments (CLIA), the College of American Pathologist (CAP), and the Clinical Laboratory Evaluation Program (CLEP). We sequenced over 7000 human vaginal samples with this pipeline and described general findings and comparisons to US census data.
ISSN:2075-4418
2075-4418
DOI:10.3390/diagnostics14182039