Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors

Christel Chehoud, Daniel J. Stieh, Aubrey G. Bailey, Alice L. Laughlin, Shannon A. Allen, Kerrie L. McCotter, Scott A. Sherrill-Mix, Thomas J. Hope, Frederic D. Bushman

We sought to investigate the effects of HIV infection on the vaginal microbiota, and associations with treatment and demographic factors. We thus compared vaginal microbiome samples from HIV+ and HIV- women collected at two Chicago area hospitals. We studied vaginal microbiome samples from 178 women analyzed longitudinally (n = 324 samples), and collected extensive data on clinical status and demographic factors. We used 16S rRNA gene sequencing to characterize the bacterial lineages present, then UniFrac, Shannon Diversity and other measures to compare community structure to sample metadata. Differences in microbiota measures were modest in the comparison of HIV+ and HIV- samples, in contrast to several previous studies, consistent with effective antiretroviral therapy. Proportions of healthy Lactobacillus species were not higher in HIV-negative subjects overall, but were significantly higher when analyzed within each hospital in isolation. Rates of bacterial vaginosis (BV) were higher among African American women and HIV+ women. BV was associated with higher frequency of HIV+. Unexpectedly, African-American women were more likely to switch BV status between sampling times; switching was not associated with HIV+ status. The influence of HIV infection on the vaginal microbiome was modest for this cohort of well-suppressed urban American women, consistent with effective anti-retroviral therapy. HIV+ was found to be associated with BV. Although BV has previously been associated with HIV transmission, most of the women studied here became HIV+ many years before our test for BV, thus implicating additional mechanisms linking HIV infection and BV.