A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease

Abstract

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.

Diagnostic Stewardship Aiming at Expectorated or Induced Sputum Promotes Microbial Diagnosis in Community-Acquired Pneumonia

“…NTHi as the most prevalent CAP pathogen in our study, is in line with recent studies from Denmark [3] and Germany [17]. Traditionally, community-acquired lower respiratory tract infections in patients with structural pulmonary diseases, especially chronic obstructive pulmonary disease (COPD), are more likely to be caused by NTHi [4,18]. Of notice, we found COPD in only 27 % of patients with NTHi infection.…”

“…Pathogenesis encompasses the transmission of infectious microbes to the respiratory epithelium, and subsequently micro-aspirations to the alveoli [2]. Over decades Streptococcus pneumoniae has invariantly been reported as the most frequent pathogen in CAP, but in later years non-typeable Haemophilus in uenza (NTHi) has emerged as most frequent in some studies [3,4].…”

Diagnostic stewardship aiming at expectorated or induced sputum promotes microbial diagnosis in community-acquired pneumonia

“…Pathogenesis encompasses the transmission of infectious microbes to the respiratory epithelium, and subsequently micro-aspirations to the alveoli [ 2 ]. Over decades Streptococcus pneumoniae has invariantly been reported as the most frequent pathogen in CAP, but in later years non-typeable Haemophilus influenza (NTHi) has emerged as most frequent in some studies [ 3 , 4 ].…”

Active site architecture reveals coordination sphere flexibility and specificity determinants in a group of closely related molybdoenzymes

“…Haemophilus influenzae MtsZ (HiMtsZ), that is required for interactions of the human pathobiont H. influenzae with its host (4). H. influenzae typically persists asymptomatically in the human nasopharynx but can cause acute respiratory tract diseases such as otitis media and pneumonia and is known to worsen chronic respiratory conditions such as chronic obstructive pulmonary disease, asthma and bronchiectasis (5)(6)(7)(8). In addition, H. influenzae has also recently been identified as a major pathogen in respiratory tract co-infections in COVID-19 patients (9).…”