Nasopharyngeal Microbiota in Healthy Children and Pneumonia Patients

Abstract

bOur study is the first to compare the nasopharyngeal microbiota of pediatric pneumonia patients and control children by 454 pyrosequencing. A distinct microbiota was associated with different pneumonia etiologies. Viral pneumonia was associated with a high abundance of the operational taxonomic unit (OTU) corresponding to Moraxella lacunata. Patients with nonviral pneumonia showed high abundances of OTUs of three typical bacterial pathogens, Streptococcus pneumoniae complex, Haemophilus influenzae complex, and Moraxella catarrhalis. Patients classified as having no definitive etiology harbored microbiota particularly enriched in the H. influenzae complex. We did not observe a commensal taxon specifically associated with health. The microbiota of the healthy nasopharynx was more diverse and contained a wider range of less abundant taxa. P neumonia is the leading cause of childhood mortality worldwide, claiming 2 million lives yearly among young children (1). The etiology of pediatric pneumonia is complex and not routinely determined in clinical practice (2). Its definitive determination remains challenging (3). Clinical research shows that Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus are the leading pathogens of bacterial pneumonia (1, 4). Respiratory syncytial virus (RSV), parainfluenza, and influenza viruses are the main causes of pediatric viral pneumonia (e.g., see references 5 and 6). S. pneumoniae and H. influenzae frequently colonize the nasopharynx of young children, and the nasopharyngeal (NP) carriage of S. pneumoniae is considered key to pneumonia and other pneumococcal diseases (7). However, the mere nasopharyngeal presence of bacterial pathogens does not necessarily lead to invasive lung infection. Various mechanisms, such as competition with resident nonpathogenic microbiota, viral coinfection, or host immune factors are likely to affect the transition from nasopharyngeal colonization to pneumonia (8). The increasing accessibility of culture-independent sequencing methods has permitted microbiota description at various body sites (9), and the potential of commensal microbiota to modify the disease process is receiving increasing attention (10).Previous culture-independent studies of the nasopharyngeal microbiota of young children looked at healthy children (11) and compared the microbiota composition of healthy children and children with acute otitis media (12). In the present study, we analyzed the nasopharyngeal microbiota composition, including the presence of respiratory viruses, in pediatric pneumonia patients and matched healthy controls and looked for microbiota associations with the disease status. MATERIALS AND METHODS Patients and clinical samples.A prospective case-control study conducted in 2008 to 2009 in 3 major hospitals in Switzerland (Geneva, Lausanne, and Sion) to investigate pediatric community-acquired pneumonia etiology was described in detail elsewhere (13). Briefly, pneumonia cases were diagnosed according to the WHO criteria (14) in children 2 ...

Respiratory microbiota and lower respiratory tract disease

“…46,66 Veillonella and Dolosigranulum were frequently sequenced in healthy individuals or patients with less severe pneumonia in upper respiratory tract samples, the latter particularly in young children. 46,66,67,73 Interestingly, despite Moraxella being associated with pneumonia, Moraxella lacunata was significantly more frequent in pediatric viral vs. non-viral pneumonia, and more frequent in controls than in all-cause pneumonia, highlighting the necessary caution in establishing associations based on phylum or genera-level taxonomics. 67 Interesting inconsistencies merit further examination.…”

“…46,66,67,73 Interestingly, despite Moraxella being associated with pneumonia, Moraxella lacunata was significantly more frequent in pediatric viral vs. non-viral pneumonia, and more frequent in controls than in all-cause pneumonia, highlighting the necessary caution in establishing associations based on phylum or genera-level taxonomics. 67 Interesting inconsistencies merit further examination. In a study in adults with community-acquired pneumonia and healthy controls, oropharyngeal microbiota dominated by Lactobacillales (predominantly Streptococcus spp.)…”

Early-Life Intranasal Colonization with Nontypeable Haemophilus influenzae Exacerbates Juvenile Airway Disease in Mice

“…The description of the infant respiratory microbiome is only just beginning (45,56,57), but a recent study found an association between early-life H. influenzae nasopharyngeal colonization and microbial population perturbations brought on by viral infection and antibiotic treatment (49). A long-term study performed in Denmark showed that children who exhibited signs of asthma and wheezing by age 7 years had an abnormal immune response to H. influenzae at age 6 months, as measured by cytokine levels and T-cell responses in stored peripheral blood mononuclear cells (PBMCs) obtained from the study participants.…”

Upper Respiratory Dysbiosis in Children

“…Обобщая литературные данные по микро-биоценозу носоглотки детей, можно выделить следующие таксономические группы [23, [26].…”