title: THE ROLE OF THE VAGINAL MICROBIOME IN HPV INFECTION AND CARCINOGENESIS
Creators: name: Gill, AC
Publisher: name: University of Liverpool Repository
Year: 2018

description: THE ROLE OF THE VAGINAL MICROBIOME IN HPV INFECTION AND CARCINOGENESIS by Alessandra Christina Gill Cervical cancer is one of the most common cancers affecting women worldwide and is caused by persistent infection with high-risk types of human papillomavirus (HR- HPV). Cervical cancer rates are particularly high in developing regions, including South Africa, which currently also has the highest HIV prevalence anywhere in the world. The immunosuppression associated with HIV infection results in an increased likelihood of persistent HR-HPV infection in HIV-positive women, resulting in an increased risk of progression to cervical cancer, a risk that increases as HIV infection progresses. Another risk factor for HR-HPV infection is a condition called bacterial vaginosis (BV) which is typified by a vaginal microbiome (VMB) made up of a diverse array of anaerobic bacteria with low numbers of lactobacilli. However, little detail is known about the bacterial species that are involved and the mechanisms that underlie this association. Using samples collected by the HARP (HPV in Africa Research Partnership) study, which was coordinated by the London School of Hygiene and Tropical Medicine, this study aimed to determine the association between the type of VMB and high-risk HPV infection and the presence of precancerous lesions of the cervix in HIV-infected South African women. This was achieved by characterising the VMB with the help of 16S rRNA gene sequencing of the V3-V4 region on the Illumina HiSeq platform, allowing identification of the bacterial taxa present in each vaginal sample. Laboratory and computational methods were optimised prior to sequencing of clinical samples to optimise the information gained. We were able to determine that samples collected during the HARP study in the fixative medium BoonFix® and stored at room temperature were suitable for microbiome analysis. Furthermore, when using the Qiagen Blood and Tissue Kit, the inclusion of the collected vaginal swab in the proteinase K digestion step significantly increased DNA yield, which was correlated with lower levels of contaminant reads in the sequencing results. In order to further refine the sequencing results, we tested two newer OTU clustering methods (DADA2 and Swarm) against USEARCH and were able to show that newer methods allow better ii species separation than those (such as USEARCH) that rely on a similarity threshold. We found that this population of HIV-positive South African women had VMB profiles typical for women with black ethnic background and HIV infection: the majority had a Lactobacillus iners-dominated community, had a microbiome consisting of a diverse mixture of anaerobes typically associated with BV, or lay somewhere between these two extremes having lower levels of L. iners together with BV-associated anaerobes. In contrast, community types dominated by L. crispatus, L. jensenii, Gardnerella vaginalis, Atopobium vaginae or Bifidobacterium spp., or containing a relatively high abundance of pathobionts such as streptococci, staphylococci or Enterobacteriaceae, were uncommon or rare. Our results provide evidence for an association between HR-HPV infection and a high diversity vaginal microbiota typical of BV with a paucity of lactobacilli in general but especially L. crispatus. However, the effect sizes were relatively small in comparison to other studies, which may be due to the fact that our entire study population was HIV- positive: these women had a high baseline prevalence of non-lactobacilli-dominated VMBs (43% had a Nugent score of 7-10) and were more vulnerable to acquisition and persistence of pathogens (due to a median CD4 count of only 428 cells/μl) than HIV-negative women in the general population. In multivariable models, we found no evidence of an association between the VMB and histological precancerous changes of the cervix in this cohort, beyond that related to persistent HR-HPV infection. The results of this study suggest that a high diversity vaginal microbiome with a paucity of lactobacilli is associated with HR-HPV infection in HIV-positive women and highlight the importance of taking HIV status into account when researching the VMB in HR-HPV infection and associated precancerous changes. A better understanding of how the vaginal microbiome impacts on the natural history of HPV infection and cervical cancer in women living with HIV could ultimately lead to improved management and treatment of these conditions in this high-risk group.