The nasopharyngeal microbiome and LRTIs in infants

Acute lower respiratory tract infections (LRTIs) are a major source of early life morbidity and the principal infectious cause of infant mortality.1 A growing body
of research suggests that the microbiome of the upper respiratory tract substantially influences the incidence and severity of LRTIs. The nasopharyngeal mucosa is the first line of defence against airborne pathogens. In addition to the mechanisms of host innate immunity, the commensal microbiota suppresses the expansion of populations of opportunistic pathogens that are common in the nasopharynx—including Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus—through a combination of competitive exclusion,
suppression of virulence through direct interspecies interaction, and regulation of local immunity.2 Opportunistic pathogens thus have to overcome both host defences and the stabilising effects of the commensal microbiota to proliferate within the upper airways.