Oncogenic human papillomavirus and anal microbiota in men who have sex with men and are living with HIV in Northern Taiwan

Abstract

Few studies have demonstrated the interplay between human immunodeficiency virus (HIV), anal human papillomavirus (HPV), and anal microbiota, especially in persons living with HIV who are men who have sex with men. We, therefore, explored these interrelationships in a cohort of persons living with HIV, mainly comprising men who have sex with men. HPV genotyping using a commercial genotyping kit and ThinPrep cytology interpreted by Bethesda systems was performed on samples from 291 patients. Samples were characterized by high-throughput sequencing of dual-index barcoded 16s rRNA (V3-4). Bacterial diversity was diminished in individuals living with HIV with CD4+ T cells <500 cells/μL and anal cytology yielding atypical squamous cells of undetermined significance or higher grades (ASCUS+) with detectable HPV 16/18 compared with those with CD4+ T cells ≥500 cells/μL with ASCUS+ and HPV 16/18 and those with normal anal cytology or inflammation without HPV 16/18. Enterobacteriaceae, Ruminococcus, and Bacilli were significantly abundant in persons living with HIV with CD4+ T cells <500 cells/μL with ASCUS+ and HPV 16/18. Bacterial diversity, composition, and homogeneity of dispersion were different in individuals living with HIV with low CD4+ T cells with ASCUS+ and HPV 16/18, and understanding the interaction among immunocompromised hosts, oncogenic HPVs, and microbiota is essential, and the contribution of these factors to anal precancerous lesions needs more in-depth exploration.

Fig 1. Grouping of anal samples according to cytology, HPV 16/18, and CD4+ T cell counts.

ASCUS, atypical squamous cells of undetermined significance; Gr, group; HPV, human papillomavirus; MSM-LWH, men who have sex with men and live with HIV.

Fig 2. Alpha diversity comparing group 1 and groups 2, 3, 4, 5, and 6.

Observed p = 0.033 for group 1 vs. group 2, p = 0.022 for group 1 vs. group 6; Chao1 p = 0.053 for group 1 vs. group 6, all by Wilcoxon–Mann–Whitney tests. Note: group 1: PLWH whose CD4+ T cell counts were < 500 cells/μL with anal cytology yielding ASCUS+ and detectable HPV 16/18 (n = 21); group 2: PLWH whose CD4+ T cell counts were ≥ 500 cells/μL with anal cytology yielding ASCUS+ with detectable HPV 16/18 (n = 25); group 3: PLWH who had anal cytology yielding ASCUS+ without HPV 16/18 detection (n = 87), group 4: PLWH whose CD4+ T cell counts were < 500 cells/μL and who had normal anal cytology or inflammation with detectable HPV 16/18 (n = 13); group 5: PLWH whose CD4+ T cell counts were ≥ 500 cells/μL and who had normal anal cytology or inflammation with detectable HPV 16/18 (n = 9); and group 6: PLWH who had normal anal cytology or inflammation without HPV 16/18 detection (n = 136). ASCUS, atypical squamous cells of undetermined significance; Gr, group; HPV, human papillomavirus; PLWH, persons living with HIV.

Fig 3. Beta diversity comparing group 1 and groups 2, 3, 4, 5, and 6.

3a: PcoA on unweighted UniFrac: Betadisper test p = 0.038 (group 1 vs. group 5), Adonis p = 0.014 (group 1 vs. group 6); 3b: no significance; 3b: PcoA on variance adjusted weighted UniFrac: Adonis p = 0.017 (group 1 vs. group 6); 3c: PcoA on GuniFrac with alpha 0.5: Adonis p = 0.030 (group 1 vs. group 6); and 3d: NMDs on Bray–Curtis distance: Adonis test p = 0.0639 (group 1 vs. group 2); Adonis test 0.0149 (group 1 vs. group 3); Adonis tests p = 0.0006 (group 1 vs. group 6). Note: group 1: PLWH whose CD4+ T cell counts were < 500 cells/μL with anal cytology yielding ASCUS+ and detectable HPV 16/18 (n = 21); group 2: PLWH whose CD4+ T cell counts were ≥ 500 cells/μL with anal cytology yielding ASCUS+ with detectable HPV 16/18 (n = 25); group 3: PLWH who had anal cytology yielding ASCUS+ without HPV 16/18 detection (n = 87), group 4: PLWH whose CD4+ T cell counts were < 500 cells/μL and who had normal anal cytology or inflammation with detectable HPV 16/18 (n = 13); group 5: PLWH whose CD4+ T cell counts were ≥ 500 cells/μL and who had normal anal cytology or inflammation with detectable HPV 16/18 (n = 9); and group 6: PLWH who had normal anal cytology or inflammation without HPV 16/18 detection (n = 136). ASCUS, atypical squamous cells of undetermined significance; Gr, group; HPV, human papillomavirus; NMDs, Non-metric Multidimensional Scaling; PcoA: Principal Co-ordinates Analysis; PLWH, persons living with HIV.

Fig 4. Linear discriminant analysis effect size comparing group 1 and groups 2, 3, 4, 5, and 6 and cladogram.

4a: group 1 vs. group 2; 4b: group 1 vs. group 3; 4c: group 1 vs. group 4, 4d: group 1 vs. group 6. Note: group 1: PLWH whose CD4+ T cell counts were < 500 cells/μL with anal cytology yielding ASCUS+ and detectable HPV 16/18 (n = 21); group 2: PLWH whose CD4+ T cell counts were ≥ 500 cells/μL with anal cytology yielding ASCUS+ with detectable HPV 16/18 (n = 25); group 3: PLWH who had anal cytology yielding ASCUS+ without HPV 16/18 detection (n = 87), group 4: PLWH whose CD4+ T cell counts were < 500 cells/μL and who had normal anal cytology or inflammation with detectable HPV 16/18 (n = 13); group 5: PLWH whose CD4+ T cell counts were ≥ 500 cells/μL and who had normal anal cytology or inflammation with detectable HPV 16/18 (n = 9); and group 6: PLWH who had normal anal cytology or inflammation without HPV 16/18 detection (n = 136). ASCUS, atypical squamous cells of undetermined significance; Gr, group; HPV, human papillomavirus; PLWH, persons living with HIV.