Microbial diversity, otitis media, and the pneumococcal transctiptome

描述（由申请方提供）：肺炎链球菌无症状地定植于健康幼儿的上呼吸道，是急性中耳炎（OM）的主要原因。S.肺炎菌定殖是疾病过程中的关键步骤，并且发生在复杂微生物群落的背景下。对细菌定植模式与OM风险之间关系的了解有限，阻碍了预防和治疗策略的发展，这些策略可最大限度地提高临床结局，并最大限度地减少对保护性植物植物群的破坏。我们提出的研究是对NIDCD计划公告（PA-08-092）“研究多微生物疾病的新方法”的直接响应。我们将分析来自249名6个月至3岁以下费城儿童的横断面研究的现有数据。在2009-10年冬季呼吸道病毒季节收集样本和数据。高通量454 16 S rRNA基因焦磷酸测序将用于表征鼻腔微生物群落。将使用Illumina Genome Analyzer 2平台上的RNA测序（RNA-seq）比较S. pneumoniae的转录谱。我们的具体目标是：1）表征健康儿童、患有急性OM的儿童和患有其他主要非细菌性上呼吸道感染的儿童的横截面样品中的上呼吸道微生物群落结构，其通常在急性OM发作之前，和2）开发RNA-seq方案和生物信息学管道以研究S. pneumoniae的转录谱，单独和在关键物种的存在下。这些研究将确定参与沙门氏菌致病途径的正常植物群的成员。肺炎定植和急性OM。新的方法将被开发用于鉴定S。在多微生物环境中唯一表达的肺炎毒力基因。从长远来看，这些数据将有助于开发生物治疗药物，如益生菌，还将提供与控制呼吸道定植的其他细菌病原体相关的信息。 公共卫生相关性：这项研究将阐明上呼吸道微生物群落组成与肺炎球菌定植和中耳炎风险之间的关系。研究结果将有助于制定常见细菌病原体的预防策略。

DESCRIPTION (provided by applicant): 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.