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UBC Theses and Dissertations

Profiling the vaginal microbiome in HIV-positive women Mahal, Daljeet Singh


Disruptions or imbalances of the vaginal microbiome can lead to negative reproductive health consequences for women, including an increased risk of sexually transmitted infections, pelvic inflammatory disease, and preterm birth. HIV-positive women may be particularly vulnerable to microbiome disruptions due to the immune dysfunction intrinsic to this disease. The objective of this study was to explore the vaginal microbiome in HIV-positive reproductive-aged women utilizing cpn60 metagenomic profiling and to correlate vaginal bacterial profiles with demographic/clinical variables. 54 HIV-positive women were recruited from the Oak Tree Clinic in Vancouver, BC. Demographic/clinical information was collected and vaginal gram-stains were assessed by Nugent’s scoring. Total DNA was extracted from vaginal swabs and PCR amplified using cpn60-specific universal primers. Cpn60-sequence libraries were generated with 454-GS-FLX Titanium pyrosequencing. 64 unique bacterial phylotypes were classified based on sequence similarity to known bacterial organisms and 10 common vaginal community clusters were generated. Fisher’s exact test and Wilcoxon signed-rank tests were utilized to conduct statistical analyses. The mean age of enrolled women was 36.6 years (range=22.3–48.8). The mean CD4 count for these women was 484 cells/mm³ (range=90-930 cells/mm³) while the mean viral load was 13,144 copies/mL (range=<40-355,245 copies/mL). 63% of women had suppressed viral loads while 85% of women were on antiretroviral therapy. According to scored vaginal Gram stains, 30% (16/54) of women had bacterial vaginosis and 11% (6/54) had intermediate scores. 12/54 women were categorized as having abnormal vaginal discharge. Abnormal vaginal discharge significantly correlated with Dialister micraerophilus, Gardnerella vaginalis B, Gardnerella vaginalis D, Porphyromonas uenonis, Prevotella amnii, Prevotella buccalis, and Prevotella timonensis (p<0.04 for all). Normal vaginal discharge significantly correlated with Lactobacillus crispatus (p<0.0006). Viral loads <40 copies/mL significantly correlated with Lactobacillus crispatus and Lactobacillus gasseri while viral loads >40 copies/mL correlated with Atopobium vaginae, Gardnerella vaginalis D, Prevotella amnii, and 4 other potentially novel bacterial species (P<0.03 for all). CD4 counts <350 cells/mm³ significantly correlated with Gardnerella vaginalis B and Lactobacillus iners (p<0.05 for all). Cpn60-based sequence data demonstrated substantial variation in the vaginal microbiome among HIV-positive women, with species-specific differences dependent on vaginal discharge status, immune status and uncontrolled HIV replication.

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