High-Risk Human Papillomavirus Persistence and Anal Microbiota Among Nigerian Men Who Have Sex With Men Living With or At Risk for HIV

PURPOSE Noninvasive therapies, such as probiotics that promote local immunity and reduce persistence of high-risk human papillomavirus (HR-HPV), would circumvent challenges in implementing anal cancer screening where same-sex behavior is stigmatized and criminalized. We describe the persistence of HR-HPV and its relationship with the anal microbiota among Nigerian men who have sex with men (MSM). METHODS Anal swabs from HIV-uninfected and -infected MSM who were enrolled in the TRUST/RV368 cohort were HPV genotyped at enrollment and at 3 and 12 months. Participants who presented with the same type(s) of HR-HPV across all visits were categorized as having persistent infections. The anal microbiota composition at baseline of HR-HPV–positive individuals was evaluated. Unsupervised K-means clustering of the 15 most abundant bacterial taxa identified 2 microbial clusters (MC-1 and MC-2). Unadjusted associations of 12-month HR-HPV persistence was evaluated by MC membership and HIV status using χ2 tests and logistic regression. RESULTS One hundred nine HIV-infected and 41 HIV-uninfected participants—contributing 284 baseline HR-HPV infections—were observed for a median of 12 months (interquartile range, 11.5-12.6 months). MC-1 was dominated by Prevotella and MC-2 consisted of a diverse set of anaerobic bacteria ( Finegoldia, Corynebacterium, Peptoniphilus, and Anerococcus). At 12 months, 45% (67 of 150) of MSM had 86 persistent HR-HPV and 55% (83 of 150) cleared all baseline HR-HPV. HPV16 (21%), HPV45 (13%), and HPV51 (12%) were the most persistent. Persistence of any HR-HPV was nonsignificantly higher in MC-1 (odds ratio [OR], 1.6; 95% CI, 0.8 to 3.1). Persistent HPV16 was more abundant in MC-2 versus MC-1 (OR, 3.9; 95% CI, 1.2 to 12.0), whereas HPV45 and HPV51 were similarly distributed across both MCs. Compared with HIV-uninfected, persistence (OR, 1.6; 95% CI, 0.8 to 3.3) and MC-2 membership (OR, 1.3; 95% CI, 0.8 to 2.0) were nonsignificantly higher among HIV-infected participants. CONCLUSION Anal HPV16 has the highest annual persistence and is associated with a low Prevotella anal microbiota, a potentially modifiable cofactor.