Nearly two-thirds of new HIV infections in sub-Saharan Africa occur in women, and a woman’s vaginal microbiome can influence her risk. In particular, an overgrowth of bacteria called bacterial vaginosis, or BV, raises HIV risk.
But not all BV-associated microbes raise HIV risk to the same degree. New work, published today in The Journal of Infectious Diseases, Fred Hutch Cancer Center scientists and a team of investigators from around the world report 14 BV-associated bacteria — and one immune protein — that put women at highest risk of HIV infection.
“The findings have several implications, particularly for prevention,” said Fred Hutch microbiologist David Fredricks, MD, whose lab helped to generate the data used in the study. “These markers could be used in risk stratification, for identifying women at highest risk of acquiring HIV.”
Once identified, these women could be guided to interventions, such as pre-exposure prophylaxis (PrEP) or antibiotic treatment, that may help reduce their HIV risk, he said.
While other studies have examined the relationship between the vaginal microbiome and HIV infection, the current work is one of the few studies to characterize the vaginal microbiome prior to detection of HIV. It’s also the largest study that assesses how both inflammatory markers and the makeup of the vaginal microbiome contribute to HIV risk.
Fredricks has long been interested in the interplay of complex microbial communities, and how one set of microbes (such as those populating the vagina) influence how likely someone is to become infected with another microbe (in this case, HIV). But whether in balance or out of balance, as in BV, microbiomes are never simple.
“It’s not like tuberculosis, which is caused by one microbe,” Fredricks said. “Bacterial vaginosis is a whole community of bacteria, and it differs from woman to woman.”
Microbiomes are so multi-dimensional that Fredricks and his team continually discover new species, including BV-associated Megasphaera hutchinsoni that they named in honor of Fred Hutch.
But this complexity means that it is frustratingly difficult to untangle which vaginal microbes influence HIV risk.
“One of the challenges with microbiome science in general is that it's frustratingly not reproducible,” Fredricks said. The microbes causing BV in one woman may differ from those causing BV in another — and those different communities influence HIV risk to different degrees.
In a previous study looking at women living in several East African countries, he and Fred Hutch microbiologist and Principal Staff Scientist Sujatha Srinivasan, PhD, identified seven BV-associated bacterial species that appear to raise HIV risk.
“But we needed to answer the question, ‘Is this real? Is it reproducible? And are there geographical differences?’” said Srinivasan, who spearheaded the work.
Fred Hutch file photos
To get these answers, she, Fredricks and their team turned to vaginal swabs collected as part of the National Institutes of Health-funded VOICE (Vaginal and Oral Interventions to Control the Epidemic) study, a randomized clinical trial that tested the how well different prophylactic drug formulations prevented HIV in women in South Africa, Uganda, Zambia and Zimbabwe.
Unfortunately, a lower-than-hoped-for adherence to the preventive regimens meant that more women than expected became infected with HIV during VOICE, which ran from 2009 to 2012. But more cases of HIV provide stronger underpinnings to statistical associations between various bacteria and HIV risk. The investigators were able to examine samples from 586 women, 150 of whom acquired HIV while participating in the study.
“We also asked, ‘What else do we need, to predict risk?’” Srinivasan said. “We decided to include the host biomarkers.”
Collaborators and co-authors include VOICE’s principal investigator, Sharon Hillier, PhD, at the Magee-Womens Research Institute & Foundation, and Jeanne Marrazzo, MD, MPH, who co-chaired the VOICE protocol and directs the National Institute of Allergy and Infectious Diseases.
Participants were negative for HIV when they entered the VOICE study, allowing Srinivasan the chance to examine their vaginal microbiota prior to HIV infection. She was able to compare the vaginal microbiomes of women with BV who remained HIV negative to the microbiomes of women who had BV and became HIV positive.
First, the scientists cast a wide net, looking for bacterial taxa (a large category of related species) found in BV that associated with higher HIV risk.
“We found that specificity really matters,” Srinivasan said. “A particular assay may detect bacteria that are very closely related from an evolutionary standpoint, but they may be acting very differently.”
She also developed methods to measure the levels of specific risk-associated bacteria to see whether higher abundance raised HIV risk further.
They combined their surveys of bacteria with assessment of inflammation markers, including certain pro-inflammatory immune proteins.
When the scientists took a bird’s eye view of women’s bacterial communities, they appeared roughly similar. But when the researchers homed in on specific BV-associated bacteria, they saw strong associations with increased HIV risk.
“What we found was that there was a whole host of bacteria that were associated with elevated risk of HIV infection amongst the BV-associated bacteria,” Fredricks said.
They identified 14 BV-associated bacterial taxa and six inflammatory proteins that, at high concentrations, were associated with increased risk of HIV infection. These taxa included those identified in the earlier study, helping to confirm those findings. The size of the study also enabled them to identify new bacterial taxa associated with HIV acquisition risk such as Amygdalobacter indicium and Megasphaera hutchinsoni.
Women who had all 14 taxa and all six immune markers were at much higher risk of HIV infection than women without these markers. A particular immune protein, called IP-10, combined with all 14 bacterial taxa distinguished women at highest risk. The fact that one inflammatory protein stood out was somewhat surprising, the investigators said.
They also highlighted one bacterial species, Lactobacillus crispatus, associated with protection from HIV infection in their analysis.
Now that the association between certain BV bacteria and HIV risk is solidified, the scientists hope their findings could one day help guide prevention efforts.
Health clinics can already test for STDs like chlamydia, so it would be possible to develop a test for the highest-risk bacteria that helps identify women who would most benefit from preventive strategies like PrEP. Long-acting formulations of HIV-preventive antivirals developed since VOICE can help improve adherence and efficacy.
“We also found that most of these bacteria are susceptible to the antibiotic metronidazole,” Fredricks said. “That sets up the potential in the future that we might be able to reduce the risk of HIV acquisition by eradicating some of these high-risk bacteria with antibiotic therapy.”
L. crispatus, the bacterial species linked to protection against HIV, has been tested in a clinical trial as a way to prevent BV recurrence after antibiotic treatment. Whether this bacterial probiotic works to reduce risk of HIV acquisition remains to be seen. Scientists are also exploring whether treating people with combinations of beneficial microbes may be a better way to reshape their microbiomes and promote long-term health, Fredricks said.
In the short term, Srinivasan is chasing down how and why certain bacteria and immune proteins raise HIV risk when others don’t.
“We don’t know what the causal factors are,” she said. “We want to try and understand the mechanisms as a foundation for thinking about whether there are other interventions we could use to reduce HIV risk.”
This work was funded by the National Institute of Allergy and Infectious Diseases, the Eunice Kennedy Shriver National Institute of Child Health and Human Development, the National Institute of Mental Health and the University of Washington’s Center for AIDS Research.
Sabrina Richards, a staff writer at Fred Hutchinson Cancer Center, has written about scientific research and the environment for The Scientist and OnEarth Magazine. She has a PhD in immunology from the University of Washington, an MA in journalism and an advanced certificate from the Science, Health and Environmental Reporting Program at New York University. Reach her at srichar2@fredhutch.org.
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