The demographics and comorbidities of patients with community acquired pneumonia (CAP) vary enormously but stratified treatment is difficult because aetiological studies have failed to comprehensively identify the pathogens. Our aim was to describe the bacterial microbiota of CAP and relate these to clinical characteristics in order to inform future trials of treatment stratified by co-morbidity. CAP patients were prospectively recruited at two UK hospitals. We used 16S rRNA gene sequencing to identify the dominant bacteria in sputum and compositional data analysis to determine associations with patient characteristics. We analysed sputum samples from 77 patients and found a Streptococcus sp. and a Haemophilus sp. were the most relatively abundant pathogens. The Haemophilus sp. was more likely to be dominant in patients with pre-existing lung disease, and its relative abundance was associated with qPCR levels of Haemophilus influenzae. The most abundant Streptococcus sp. was associated with qPCR levels of Streptococcus pneumoniae but dominance could not be predicted from clinical characteristics. These data suggest chronic lung disease influences the microbiota of sputum in patients with CAP. This finding could inform a trial of stratifying empirical CAP antibiotics to target Haemophilus spp. in addition to Streptococcus spp. in those with chronic lung disease.
Bibliographical noteFunding Information:
We would like to thank the patients who volunteered for the study, the NIHR for funding the work and the NIHR Clinical Local Research Network (CLRN) for providing strategic support for recruitment. We would also like to thank Professor Craig Winstanley for his critical appraisal of the manuscript. The study was funded by a UK National Institute of Health Research (NIHR) Doctoral Research. Fellowship (DRF-2010-03-154) with support from the North West Clinical Research Network (NW-CLRN).
© 2019, The Author(s).