Abstract Rationale People living with HIV are at increased risk of respiratory infections. The nasopharyngeal microbiome plays an important role in resisting colonization by respiratory pathogens that cause infection. While other microbial communities are altered in people living with HIV, the association between HIV infection and nasopharyngeal microbiome composition in adult women is poorly understood. Methods Nasopharyngeal swabs were collected from mothers and children enrolled in a cross-sectional study in Gaborone, Botswana between 2020 and 2021. After the specimens underwent shotgun metagenomic sequencing, data were processed using the nf-core/taxprofiler Nextflow pipeline. Alpha diversity measures were compared by HIV status using Wilcoxon rank-sum testing, linear regression, and ANOVA with a TukeyHSD correction for multiple comparisons to examine interactions. PERMANOVA was used to test for differences in nasopharyngeal microbiome community composition by HIV status. Differentially abundant species were identified with ANCOM-BC and p-values were adjusted using the Benjamini-Hochberg method to control the false discovery rate (FDR). Effect sizes were estimated as bias-corrected log fold changes (LFC). Analyses were adjusted for potential confounders, including wood smoke exposure and season of enrollment. Results Of 144 women enrolled in this study, 141 (98%) had nasopharyngeal samples that generated sufficient sequencing reads. The median (interquartile range, IQR) age of study participants was 29 (25, 35) years and 91 (65%) were living with HIV. Among women living with HIV, 89 (98%) were receiving antiretroviral therapy and 71/80 (89%) with HIV RNA measurements were virally suppressed (HIV RNA 400 copies/mL). The median (IQR) CD4+ cell count among women living with HIV was 676 cells/mm3 (423, 818). Nasopharyngeal microbiome alpha diversity measures, including observed species counts and Shannon index, did not differ by HIV status. However, overall microbiome composition did differ significantly by HIV status (PERMANOVA: R2=0.009 p = 0.034). Figure 1 shows the relative abundances of eight taxa which were higher among women living with HIV, including the respiratory pathogen Moraxella catarrhalis (LFC difference: 1.870, p: 0.016), and the opportunistic pathogen Acinetobacter schindleri (LFC difference: 1.115, p: 0.028). Conclusion We identified differences in nasopharyngeal microbiome composition by HIV status among adult women in Botswana. In addition to differences in global microbiome composition, Moraxella catarrhalis and Acinetobacter schindleri were more abundant in women living with HIV, which is notable due to their pathogenic potential. Further research is needed to determine if alterations in nasopharyngeal microbiome composition affect respiratory infection risk in women with HIV. This abstract is funded by: National Institutes of Health (R25-AI140495, K23-HL166022, D43 TW009337, 5P30-AI064518, P30-AI045008).
Wilson et al. (Fri,) studied this question.