Respiratory tract infections cause a great burden on children under 2 years of age. Most respiratory tract infections are caused by viruses, but co-infections with viruses and bacteria are common. The aims of these studies were to assess inhibiting and synergistic interactions between respiratory viruses and bacteria, to analyze the effects of genetic variants in the host innate immune system and to determine the effects of vaccination with a pneumococcal conjugate vaccine on viral and bacterial diseases and bacterial colonization in children. 

We followed 923 children in a prospective cohort study for respiratory tract infections during the years 2008-2012 by symptom diaries, nasal swab samples and clinical examinations. Viruses and bacteria were analyzed during respiratory tract infections and at certain ages when children were healthy. Genetic polymorphisms of mannose-binding lectin and Toll-like receptors were determined in blood samples. 

Infants with genetic polymorphisms of mannose-binding lectin were more prone to be colonized with Streptococcus pneumoniae during rhinovirus infection. Furthermore, rhinovirus infection increased the rate of community acquisition and transmission of pneumococcus in families with children. The rate of rhinovirus infections was significantly lower during respiratory syncytial virus infection compared to control children suggesting inhibiting interaction between these viruses. In a cluster randomized trial, 10-valent pneumococcal conjugate vaccine prevented not only acute otitis media but to some extent also all respiratory tract infections that are mainly caused by viruses. 

These studies showed that viral infection predisposes children to bacterial colonization and synergism between viruses and bacteria is affected by genetic variations in the host immune system. However, also negative interactions between microbes occur. By affecting the microbiological environment in the nasopharynx, pneumococcal conjugate vaccines may have effect on both bacterial and viral infections.