Antibiotics at birth reshape infant mycobiota in early life

Administering azithromycin to women during labour has been shown in randomized clinical trials to reduce maternal sepsis, a leading cause of maternal mortality in low-income countries. Because azithromycin reaches the infant through breast milk, understanding its broader biological effects—including its safety for the newborn—is essential for sustainable scale-up of this potentially life-saving intervention. To date, nothing was known about how this intervention impacts the infant gut mycobiota, the community of fungi that shapes early immune and metabolic development and can influence mid- and long-term child health.We analyzed how intrapartum azithromycin affected the gut mycobiota of children up to three years of age using rectal swabs collected from a large randomized trial conducted in The Gambia, West Africa. While season and maternal factors were the strongest drivers of mycobiota composition, azithromycin exposure caused a modest, season-dependent increase in Candida orthopsilosis, which is unlikely to be clinically harmful, and had no lasting effect on overall fungal community structure.These findings provide reassuring evidence that intrapartum azithromycin is safe for newborns, causing minimal disruption to the infant fungal ecosystem. They support the continued evaluation and scale-up of this life-saving intervention while emphasizing the critical influence of environmental and maternal factors when assessing the broader effects of peripartum prophylactic antibiotics.