Streptococcus pneumoniae asymptomatically colonizes the upper respiratory tract of healthy young children and is a leading cause of acute otitis media (OM). S. pneumoniae colonization is a critical step in the disease process and occurs in the context of a complex microbial community. Limited understanding of the relationships between bacterial colonization patterns and risk of OM has hindered the development of preventive and therapeutic strategies that maximize clinical outcomes and minimize disruptions to the protective commensal flora. Our proposed studies are in direct response to the NIDCD Program Announcement (PA-08-092) "Novel Approaches to Study Polymicrobial Diseases". We will analyze pre-existing data from a cross sectional study of 249 Philadelphia children 6 months to =3 years of age. Samples and data were collected during the 2009-10 winter respiratory virus season. High throughput 454 16S rRNA gene pyrosequencing will be used to characterize nasal microbial communities. RNA-sequencing (RNA-seq) on the Illumina Genome Analyzer 2 platform will be used to compare S. pneumoniae transcriptional profiles under a range of experimental conditions.
Our specific aims are: 1) To characterize upper respiratory tract microbial community structure in a cross sectional sample of healthy children, children with acute OM, and children with other, primarily non-bacterial upper respiratory tract infections, which often precede the onset of acute OM and 2) To develop RNA- seq protocols and bioinformatics pipelines to study S. pneumoniae transcriptional profiles, alone and in the presence of key commensal species. These studies will identify members of the normal flora involved in the causal pathogenic pathway of S. pneumoniae colonization and acute OM. New methods will be developed to identify S. pneumoniae virulence genes uniquely expressed in polymicrobial settings. Over the long term these data will aid in the development of biotherapeutics such as probiotics and will also provide information relevant for the control of other bacterial pathogens that colonize the respiratory tract.

Public Health Relevance

This research will elucidate relationships among upper respiratory tract microbial community composition and risk of pneumococcal colonization and otitis media. Results will facilitate development of prevention strategies for common bacterial pathogens.

Agency
National Institute of Health (NIH)
Institute
National Institute on Deafness and Other Communication Disorders (NIDCD)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21DC011667-02
Application #
8290218
Study Section
Special Emphasis Panel (ZRG1-IDM-N (02))
Program Officer
Watson, Bracie
Project Start
2011-07-01
Project End
2013-06-30
Budget Start
2012-07-01
Budget End
2013-06-30
Support Year
2
Fiscal Year
2012
Total Cost
$207,500
Indirect Cost
$82,500
Name
Yale University
Department
Public Health & Prev Medicine
Type
Schools of Medicine
DUNS #
043207562
City
New Haven
State
CT
Country
United States
Zip Code
06520
Pettigrew, Melinda M; Marks, Laura R; Kong, Yong et al. (2014) Dynamic changes in the Streptococcus pneumoniae transcriptome during transition from biofilm formation to invasive disease upon influenza A virus infection. Infect Immun 82:4607-19
Ruohola, Aino; Pettigrew, Melinda M; Lindholm, Laura et al. (2013) Bacterial and viral interactions within the nasopharynx contribute to the risk of acute otitis media. J Infect 66:247-54