Date of Award

January 2015

Document Type

Open Access Thesis

Degree Name

Master of Public Health (MPH)


School of Public Health

First Advisor

Melinda M. Pettigrew


Background: Pnuemonia is a leading cause of morbidity and mortality worldwide and children diagnosed with asthma have been shown to be at greatly increased risk of recurrent Community-Acquired Pneumonia (CAP). CAP in asthmatic children can incur nearly double the healthcare costs and lead to poorer outcomes during the course of the pneumonia infection.

Objective: This study seeks to determine if sputum (SP) samples may be used in the pediatric population to better understand the microbiome environment during severe pneumonia in place or in conjunction with the more commonly used nasopharyngeal (NP) samples. Additionally, this study seeks to identify features of the microbiome associated with pneumonia severity in asthmatic children.

Methods: Sputum and nasopharyngeal/oropharyngeal (NP/OP) samples were collected from asthmatic children diagnosed with asthma upon admission to a hospital. Bacterial cultures for known CAP pathogens using sputum samples, and PCR detection for viral pneumonia pathogens on the NP/OP samples were performed. To study the microbiome, 16s rRNA analysis of sputum and nasopharyngeal samples was performed and analysis conducted using a variety of single and community-based analyses. Outcomes of interest were LOS > 4 days and admission to the ICU.

Results: High relative abundance of CAP pathogens, including Moraxella and Haemophilus, were associated with poorer CAP outcomes in both age groups for both ICU admission and longer LOS. Similarly, a positive sputum culture result for Staphylococcus aureus was found to be significantly associated with more severe pneumonia. Bacteroidetes was associated with shorter LOS and Rothia association with longer LOS in several of the analyses. Both conclusions are consistent with previous characterizations of the bacteria in the onset of pneumonia and asthma. Moraxella was consistently associated with longer LOS and increased risk of ICU admission, consistent with its characterization as a minor CAP pathogen, but was protective against longer LOS in the younger age group.

Conclusions: First, our study demonstrates that sputum samples may be used in a pediatric population. Our findings demonstrate that many of the microbiome features previously identified as being predictive of, or associated with, CAP, also serve to predict severe pneumonia outcomes in this pediatric population, including longer Length of Stay (LOS) and Intensive Care Unit (ICU) admission. However, certain inconsistencies in the trends in our data highlight the need to perform microbiome analyses using many different approaches to fully understand the complex relationships between the diverse commensal and pathogenic bacteria that comprise the microbiome.


This is an Open Access Thesis.