The Human Milk Microbiome and the Impact of Intrapartum Azithromycin Prophylaxis among Gambian Women

The human milk microbiome plays a crucial role in shaping early-life microbial communities. This study is based on the PregnAnZI-1 trial, a double-blind, placebo-controlled study conducted in The Gambia, where a single 2 g dose of oral azithromycin was administered to women during labour to assess its impact on maternal and neonatal infections. The trial revealed potential benefits in reducing infections, mostly in women. Before considering broader implementation of the intervention, it is critical to evaluate its effects on the milk microbiome, which have short- and long-term impact on infant health. A stepwise approach was employed. First, a methodological study optimised DNA extraction techniques for 16S and ITS sequencing. Next, a background study characterised the baseline human milk microbiome in the urban Gambian population, identifying key taxa and influencing factors. A longitudinal analysis followed, describing lactational changes in the microbiome over the neonatal period. The core investigation assessed the impact of intrapartum azithromycin prophylaxis. There was strong evidence of differences in both bacterial and fungal communities between the milk samples from women receiving intrapartum azithromycin or placebo. Milk from women in the azithromycin arm showed higher bacterial diversity across the neonatal period and higher fungal diversity in colostrum (postpartum day 3), along with a greater abundance of Brevundimonas. Finally, a nested case–control study compared milk from mothers with lactational mastitis to that of healthy controls. This analysis provided the first evidence that bacterial diversity was lower in milk samples collected before mastitis onset, suggesting that dysbiosis may precede clinical symptoms. Together, this thesis offers novel insights into the effects of intrapartum azithromycin prophylaxis and underscore the importance of future studies employing shotgun metagenomics to capture the functional and taxonomic consequences of intrapartum antibiotic exposure on bacteria, fungi, and the milk virome, and their implications for both mothers and infants.