Version 1
: Received: 10 May 2024 / Approved: 15 May 2024 / Online: 15 May 2024 (13:18:32 CEST)
How to cite:
Thomas-White, K.; Hilt, E. E.; Olmschenk, G.; Gong, M.; Philips, C.; Jarvis, C.; Sanford, N.; White, J.; Navarro, P. An Accurate Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples. Preprints2024, 2024051036. https://doi.org/10.20944/preprints202405.1036.v1
Thomas-White, K.; Hilt, E. E.; Olmschenk, G.; Gong, M.; Philips, C.; Jarvis, C.; Sanford, N.; White, J.; Navarro, P. An Accurate Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples. Preprints 2024, 2024051036. https://doi.org/10.20944/preprints202405.1036.v1
Thomas-White, K.; Hilt, E. E.; Olmschenk, G.; Gong, M.; Philips, C.; Jarvis, C.; Sanford, N.; White, J.; Navarro, P. An Accurate Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples. Preprints2024, 2024051036. https://doi.org/10.20944/preprints202405.1036.v1
APA Style
Thomas-White, K., Hilt, E. E., Olmschenk, G., Gong, M., Philips, C., Jarvis, C., Sanford, N., White, J., & Navarro, P. (2024). An Accurate Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples. Preprints. https://doi.org/10.20944/preprints202405.1036.v1
Chicago/Turabian Style
Thomas-White, K., Jennifer White and Pita Navarro. 2024 "An Accurate Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples" Preprints. https://doi.org/10.20944/preprints202405.1036.v1
Abstract
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 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 88.5%, specificity of 96.2%, and a positive predictive value of 95.8% certified by Clinical Laboratory Improvement Amendments (CLIA), the College of American Pathologist (CAP) and the Clinical Laboratory Evaluation Program (CLEP). We sequenced over 7,000 human vaginal samples with this pipeline and described general findings and comparison to US census data.
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
,
,
,
,
,
,
,
