Presentation Date
19-10-2021 12:00 AM
Description
Introduction: Bacterial Vaginosis (BV) is a common disorder associated with the vaginal microbiome characterized by the displacement of lactobacillus with an overgrowth of anaerobes. Symptomatic cases can be associated with Pelvic Inflammatory Disease (PID), complications with pregnancy, and greater susceptibility to sexually transmitted infections. In cases where antibiotics are needed to treat BV, recurrence commonly occurs within 3 months to a year. Despite the prevalence of BV, the specific mechanism associated with the onset is unclear. In this pilot study we utilized shotgun metagenomics to identify the discrete changes occurring in the vaginal microbiome leading up to the onset of BV with the goal of better understanding the etiology of BV. Methods: A cohort of women with a baseline healthy vaginal microbiome (no Amsel Criteria and Nugent Score of 0 - 3) were prospectively followed for 90 days. Vaginal samples were self- collected daily to screen for incident BV (iBV). Shotgun metagenomic sequencing was carried out retrospectively following an iBV diagnosis (two consecutive days of Nugent Score > 7). Sequencing was carried out on samples collected up to 12 days leading up to iBV as well as the day of the iBV diagnosis. Samples were sequenced using the Illumina Hiseq 4000. Sequencing data was analyzed using two methods, metagenomic assembly through the Atlas workflow 2.62a, and mapping of sequenced reads to reference databases with Biobakery 3. Discussion: Both taxonomic and functional metagenomic data highlights the community changes that occur during the onset of iBV. Taxonomic analysis showed elevated abundance of BV associated bacteria such as Gardnerella vaginalis, Prevotella bivia, and Atopobium vaginae during iBV, while the relative abundance of Lactobacillus species was strikingly diminished. Functional analysis reflects the shift in dominance to BV associated anaerobes with an increased abundance of genes associated with oxidative metabolism during BV. Conclusion: Metagenomic analysis provides a new deeper level of insight into the microbial community changes that occur leading up to the onset of iBV. 1.Beghini F, McIver LJ, Blanco-Míguez A, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife. 2021;10:e65088. Published 2021 May 4. doi:10.7554/eLife.65088 2. Bradshaw, C. S. et al. J. Infect. Dis. 193, 1478–1486 (2006). 3. Colonna C, Steelman M. Amsel Criteria. [Updated 2020 Jul 13]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2021 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK542319/ 4. Kieser S, Brown J, Zdobnov EM, Trajkovski M, McCue LA. ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data. BMC Bioinformatics. 2020 Jun 22;21(1):257. doi: 10.1186/s12859-020-03585-4. PMID: 32571209; PMCID: PMC7310028. 5. Koumans, E. H. et al. Sex. Transm. Dis. 34, 864–869 (2007) 6 .Peipert, J. F., Montagno, A. B., Cooper, A. S. & Sung, C. J. Am. J. Obstet. Gynecol. 177, 1184– 1187 (1997)
Recommended Citation
Lammons, John W.; Elnagger, Jacob H.; Toh, Evelyn; Dong, Amy; Aaron, Kristal J.; Luo, Meng; Tamhane, Ashutosh; Lefkowitz, Elliot J.; Nelson, David E.; Muzny, Christina A.; and Taylor, Christopher M., "Longitudinal Shotgun Metagenomic Analysis of the Vaginal Microbiome during the Onsetof Bacterial Vaginosis" (2021). Medical Research Day. 63.
https://digitalscholar.lsuhsc.edu/sommrd/2021MRD/Posters/63
Included in
Longitudinal Shotgun Metagenomic Analysis of the Vaginal Microbiome during the Onsetof Bacterial Vaginosis
Introduction: Bacterial Vaginosis (BV) is a common disorder associated with the vaginal microbiome characterized by the displacement of lactobacillus with an overgrowth of anaerobes. Symptomatic cases can be associated with Pelvic Inflammatory Disease (PID), complications with pregnancy, and greater susceptibility to sexually transmitted infections. In cases where antibiotics are needed to treat BV, recurrence commonly occurs within 3 months to a year. Despite the prevalence of BV, the specific mechanism associated with the onset is unclear. In this pilot study we utilized shotgun metagenomics to identify the discrete changes occurring in the vaginal microbiome leading up to the onset of BV with the goal of better understanding the etiology of BV. Methods: A cohort of women with a baseline healthy vaginal microbiome (no Amsel Criteria and Nugent Score of 0 - 3) were prospectively followed for 90 days. Vaginal samples were self- collected daily to screen for incident BV (iBV). Shotgun metagenomic sequencing was carried out retrospectively following an iBV diagnosis (two consecutive days of Nugent Score > 7). Sequencing was carried out on samples collected up to 12 days leading up to iBV as well as the day of the iBV diagnosis. Samples were sequenced using the Illumina Hiseq 4000. Sequencing data was analyzed using two methods, metagenomic assembly through the Atlas workflow 2.62a, and mapping of sequenced reads to reference databases with Biobakery 3. Discussion: Both taxonomic and functional metagenomic data highlights the community changes that occur during the onset of iBV. Taxonomic analysis showed elevated abundance of BV associated bacteria such as Gardnerella vaginalis, Prevotella bivia, and Atopobium vaginae during iBV, while the relative abundance of Lactobacillus species was strikingly diminished. Functional analysis reflects the shift in dominance to BV associated anaerobes with an increased abundance of genes associated with oxidative metabolism during BV. Conclusion: Metagenomic analysis provides a new deeper level of insight into the microbial community changes that occur leading up to the onset of iBV. 1.Beghini F, McIver LJ, Blanco-Míguez A, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife. 2021;10:e65088. Published 2021 May 4. doi:10.7554/eLife.65088 2. Bradshaw, C. S. et al. J. Infect. Dis. 193, 1478–1486 (2006). 3. Colonna C, Steelman M. Amsel Criteria. [Updated 2020 Jul 13]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2021 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK542319/ 4. Kieser S, Brown J, Zdobnov EM, Trajkovski M, McCue LA. ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data. BMC Bioinformatics. 2020 Jun 22;21(1):257. doi: 10.1186/s12859-020-03585-4. PMID: 32571209; PMCID: PMC7310028. 5. Koumans, E. H. et al. Sex. Transm. Dis. 34, 864–869 (2007) 6 .Peipert, J. F., Montagno, A. B., Cooper, A. S. & Sung, C. J. Am. J. Obstet. Gynecol. 177, 1184– 1187 (1997)