Rapid Characterization of the Vaginal Microbiome/Virome in Pregnant Women

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ABSTRACT Preterm birth (PTB), delivery occurring before 37 weeks of gestation, affects approximately 10% of births in the United States each year and is the primary cause of neonatal morbidities and mortality. Because our understanding of the causes of PTB is incomplete, we are limited in our ability to predict or prevent PTB. In our previous studies, we used high-throughput sequencing to reveal characteristics of viral and bacterial communities in the vagina are associated with PTB. These data suggest that characteristics of the vaginal microbiome may serve as biomarkers for PTB, although more studies are required. While sequencing assays have been useful in beginning to identify microbial signatures associated with PTB, the incorporation of these assays into large-scale follow up studies is limited by several factors: (i) sequencing assays are in many cases qualitative, requiring subsequent assays to quantitate the microbes, thereby depleting sample material; (ii) sequencing and qPCR assays are time-consuming, requiring weeks to obtain complete data sets from each sample; and (iii) sequencing assays are relatively expensive despite many innovations that have reduced costs. Based on our increased understanding of vaginal microbial community features associated with PTB, we presently aim to develop a single, multiplexed, targeted assay that will allow us to capture the essential features we find in sequencing assays, but it will do so more quantitatively, rapidly, and cost-effectively than sequencing. The development of this assay will allow us (and others who study the microbiome of the human female reproductive tract) to maximize resource utilization in future studies by replacing multiple sequencing and PCR tests with a single, quantitative, rapid, easy to use, less expensive assay. Furthermore, this assay may serve as a foundation for future clinical studies aimed at defining risk for PTB in pregnant women