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. 2025 Apr 26;11(1):67.
doi: 10.1038/s41522-025-00697-8.

Effect of initiation of antiretroviral drugs for HIV prevention or treatment on the vaginal microbiome of pregnant women in Malawi

Friday Saidi  1   2   3 , Lauren A Graybill  4 , Jennifer H Tang  5 , Twambilile Phanga  6 , Beteniko Milala  6 , Gabriel Banda  6 , Manley Kamija  6 , Margaret Kasaro  5 , Wilbroad Mutale  7 , Joan Price  5 , Lameck Chinula  6   5   8 , Jeffrey Stringer  5 , Mina C Hosseinipour  6   4   9 , Benjamin H Chi  5 , Jacques Ravel  10   11 , Johanna B Holm  10   11
Affiliations

Effect of initiation of antiretroviral drugs for HIV prevention or treatment on the vaginal microbiome of pregnant women in Malawi

Friday Saidi et al. NPJ Biofilms Microbiomes. .

Abstract

Lack of Lactobacillus and/or dysbiosis is linked to spontaneous preterm birth (sPTB). The impact of antiretrovirals (ARVs) for HIV treatment or prevention on the vaginal microbiome during pregnancy remains unclear. We examined vaginal microbiome changes in pregnant women in Lilongwe, Malawi. Women living with HIV (WLHIV) initiated antiretroviral therapy (ART), while HIV-negative women began oral pre-exposure prophylaxis (PrEP). Of 255 participants (191 HIV-negative, 64 WLHIV) who provided baseline vaginal swabs, 181 provided follow-up swabs one month after ARV initiation. At enrollment, WLHIV had higher Shannon diversity and were more likely to have CST IV-B than CST I or III. After ARV initiation, α-diversity decreased in WLHIV but increased in HIV-negative women. Women initiating PrEP had a lower risk of sPTB compared to WLHIV initiating ART, but transitioning to CST IV during pregnancy increased the odds of sPTB. Larger studies are needed to explore ARV impact on pregnancy outcomes.

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Conflict of interest statement

Competing interests: J.R. is co-founder of LUCA Biologics, a biotechnology company focusing on translating microbiome research into live biotherapeutics drugs for women’s health. The other authors declare no competing interests.

Figures

Fig. 1
Fig. 1
CONSORT flow diagram.
Fig. 2
Fig. 2. Community State Types (CST) and Metagenomic Assignments.
CST (A) and mgSs (B) assignments were not related to sequencing depth.
Fig. 3
Fig. 3. The proportion of the metagenomic subspecies (mgSs) in each sample.
Samples (columns) are assigned to a community state types (CST) using VALENCIA based on species compositions inferred from mgSs of vaginal microbiomes, and were colored by M0 HIV serostatus (WLHIV: Women Living With HIV). The 45 most abundant mgSs are shown.
Fig. 4
Fig. 4. Baseline Differences in Alpha Diversity and CST Distribution Between WLHIV and HIV-negative women.
Alpha-diversity is higher at M0 in WLHIV compared to HIV-negative women as measured by Shannon diversity indices (A). B CST IV-B and III were the most prevalent CSTs in WLHIV and HIV-negative women at M0, respectively. C There were more HIV-negative participants in CST I and III and more WLHIV participants in CST IV-B. (*p < 0.05, **p < 0.01, ***p < 0.001).
Fig. 5
Fig. 5. Baseline Differences in Vaginal Metagenomic Subspecies Abundances by HIV serostatus.
Metagenomic subspecies (mgSs) are associated with M0 HIV serostatus. The abundances of mgSs were significantly greater (yellow) or lower (purple) in WLHIV compared to HIV-negative women at M0. Only those with adjusted p-values < 0.01 are shown. < 0.05, **p < 0.01, ***p < 0.001).
Fig. 6
Fig. 6. Changes in Alpha Diversity at Month 1 Following ART or PrEP Initiation among WLHIV and HIV-negative Women.
A At M1 following initiation of ART, alpha diversity was 24% lower among WLHIV (p = 0.006), while (B) alpha diversity was 27% higher among HIV-negative participants at M1 after initiating PrEP (p < 0.001).
Fig. 7
Fig. 7. CST Stability and Direction of CST Shifts at Month 1 following ARV Initiation Among ART and PrEP Users.
A The proportion of participants that did not change CST after ARV initiation at M1 was similar among ART and PrEP users. B ART users that changed CSTs most frequently between M0 and M1 switched from CST IV-B to CST III. Conversely, PrEP users that changed CSTs were most likely to switch from CST III to CST IV-B.
Fig. 8
Fig. 8. Shifts in Vaginal Microbial Strain Abundance at Month 1 following ART or PrEP Initiation in Pregnant Women.
A Among pregnant WLHIV, the abundances of a four mgSs decreased at M1 after ART initiation. B Among HIV-negative pregnant women, the abundances of several mgSs increased or decreased at M1 after PrEP initiation. All taxa plotted were significant (padj < 0.05).
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