Journal Article

Cervicovaginal microbiome and natural history of HPV in a longitudinal study

Porras, Carolina, Burk, Robert D., Herrero, Rolando, Gradissimo, Ana, Safaeian, Mahboobeh, Schiffman, Mark, Usyk, Mykhaylo, Castle, Philip E., Gonzalez, Paula, Zolnik, Christine P.

2020

Overview

Human papillomavirus (HPV) infection is one of the most common sexually transmitted infections. However, only a small percentage of high-risk (HR) HPV infections progress to cervical precancer and cancer. In this study, we investigated the role of the cervicovaginal microbiome (CVM) in the natural history of HR-HPV. This study was nested within the placebo arm of the Costa Rica HPV Vaccine Trial that included women aged 18-25 years of age. Cervical samples from two visits of women with an incident HR-HPV infection (n = 273 women) were used to evaluate the prospective role of the CVM on the natural history of HR-HPV. We focus specifically on infection clearance, persistence, and progression to cervical intraepithelial neoplasia grade 2 and 3 (CIN2+). The CVM was characterized by amplification and sequencing the bacterial 16S V4 rRNA gene region and the fungal ITS1 region using an Illumina MiSeq platform. OTU clustering was performed using QIIME2. Functional groups were imputed using PICRUSt and statistical analyses were performed using R. At Visit 1 (V1) abundance of Lactobacillus iners was associated with clearance of incident HR-HPV infections (Linear Discriminant Analysis (LDA)>4.0), whereas V1 Gardnerella was the dominant biomarker for HR-HPV progression (LDA>4.0). At visit 2 (V2), increased microbial Shannon diversity was significantly associated with progression to CIN2+ (p = 0.027). Multivariate mediation analysis revealed that the positive association of V1 Gardnerella with CIN2+ progression was due to the increased cervicovaginal diversity at V2 (p = 0.040). A full multivariate model of key components of the CVM showed significant protective effects via V1 genus Lactobacillus, OR = 0.41 (0.22-0.79), V1 fungal diversity, OR = 0.90 (0.82-1.00) and V1 functional Cell Motility pathway, OR = 0.75 (0.62-0.92), whereas V2 bacterial diversity, OR = 1.19 (1.03-1.38) was shown to be predictive of progression to CIN2+. This study demonstrates that features of the cervicovaginal microbiome are associated with HR-HPV progression in a prospective longitudinal cohort. The analyses indicated that the association of Gardnerella and progression to CIN2+ may actually be mediated by subsequent elevation of microbial diversity. Identified features of the microbiome associated with HR-HPV progression may be targets for therapeutic manipulation to prevent CIN2+. ClinicalTrials.gov NCT00128661.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Adolescent / Adult / Analysis / Biology and Life Sciences / Biomarkers / Biotechnology industries / Cancer / Cervix / Cervix dysplasia / Cervix Uteri - metabolism / Cervix Uteri - microbiology / Cervix Uteri - pathology / Cervix Uteri - virology / Clinical trials / Clustering / Correlation analysis / Development and progression / Discriminant analysis / Ecology and Environmental Sciences / Epidemiology / Female / Functional groups / Fungi / Gardnerella - classification / Gardnerella - genetics / Gardnerella - metabolism / Genes / Health aspects / Health risks / Human papillomavirus / Humans / Infections / Lactobacillus - classification / Lactobacillus - genetics / Lactobacillus - metabolism / Longitudinal Studies / Mediation / Medical schools / Medicine / Medicine and Health Sciences / Microbiomes / Microbiota / Microorganisms / Multivariate analysis / Natural history / Papillomaviridae - metabolism / Papillomavirus / Papillomavirus infections / Papillomavirus Infections - metabolism / Papillomavirus Infections - microbiology / Papillomavirus Infections - pathology / Pediatrics / RNA / rRNA 16S / Sexually transmitted diseases / Statistical analysis / Statistical methods / STD / Studies / Taxonomy / Uterine Cervical Dysplasia - metabolism / Uterine Cervical Dysplasia - microbiology / Uterine Cervical Dysplasia - pathology / Uterine Cervical Dysplasia - virology / Uterine Cervical Neoplasms - metabolism / Uterine Cervical Neoplasms - microbiology / Uterine Cervical Neoplasms - pathology / Uterine Cervical Neoplasms - virology / Vaccines / Vagina - metabolism / Vagina - microbiology / Vagina - pathology / Vagina - virology / Viral infections / Women / Womens health