Haemophilus spp. is dominant among the sputum microbiota of UK adults with community acquired pneumonia.. Microbiota of Community Acquired Pneumonia

The aetiological cause of community acquired pneumonia (CAP) is often unknown. We describe the largest pyrosequencing study of acute sputum from adult patients with CAP and attempt, for the first time, to relate the spectrum of bacteria to clinical characteristics in order to inform empirical antibiotic choice.We prospectively recruited patients with CAP at two hospitals in Liverpool, UK. We obtained patients’ sputum and used 16S rRNA gene pyrosequencing to identify the bacteria in each sample. We used compositional data analysis to determine if patient characteristics could predict which bacteria would dominate each sample.We sequenced 77 sputum samples and found 4947 different bacteria and analysed the 30 whose relative abundance was most variable between samples. We found a bacteria from the genus Haemophilus spp. varied most between samples. High relative abundance of this Haemophilus correlated with a prior diagnosis of lung disease and was often not detected by sputum culture. In comparison the relative abundance of the most dominant Streptococcus spp. did not vary significantly between patients. We performed qPCRs for Haemophilus influenzae and Streptococcus pneumoniae and found that absolute concentrations of these two species correlated with the most highly abundant Haemophilus and Streptococcus respectively.The most important factor in determining which bacteria are relatively abundant in the sputum of patients with CAP is the presence of underlying lung disease. Future trials should test the benefit of modifying empirical CAP antibiotics to treat Haemophilus influenzae in addition to Streptococcus pneumoniae for those with lung disease.