BACKGROUND: Respiratory syncytial virus (RSV) is a major cause of severe respiratory infections in infants, especially under 5 years of age. Several studies have reported that interactions between RSV and bacteria like Streptococcus pneumoniae (SP), Moraxella catarrhalis (MC), Haemophilus influenzae (HI) and Staphylococcus aureus (SA) may influence their pathogenicity and the clinical outcome of infection. However, existing knowledge about RSV-bacterial interactions in infants comes primarily from cross-sectional studies, which cannot evaluate the influence of infection sequence on these interactions. METHODS: We conducted a nested prospective study of the Zambian mother-infant birth cohort, followed for the first 14 weeks of life. Nasopharyngeal samples were collected from both infants and mothers biweekly. We analyzed the sequence of RSV and bacterial detection, and its correlation with RSV and bacterial density, and with severity of symptoms. RESULTS: SP acquisition in infants following RSV infection is associated with lower bacterial densities compared to SP alone. These effects were not observed with Moraxella catarrhalis, Staphylococcus aureus or Haemophilus influenzae, or in the mothers. Additionally, prior RSV did not result in earlier bacterial acquisition. Our data suggests that prior bacterial infection with any of the species did not significantly affect RSV viral loads. Finally, antibiotic exposure in infants did not reduce bacterial density overall, but infants with SP-only infections who received antibiotics showed increased bacterial levels. CONCLUSION: The observed effect of prior RSV on SP density, which was not seen in other bacteria, suggests a specific interaction between RSV and SP that may influence bacterial colonization dynamics differently than other bacterial species, highlighting the need for further investigation into these mechanisms.