Microbial diversity, otitis media, and the pneumococcal transctiptome

描述（由申请人提供）：肺炎链球菌在健康幼儿的上呼吸道无症状地定植，是急性中耳炎（OM）的主要原因。肺炎链球菌定植是疾病过程中的关键步骤，发生在复杂的微生物群落背景下。对细菌定植模式和OM风险之间关系的有限理解阻碍了预防和治疗策略的发展，这些策略可以最大限度地提高临床效果并最大限度地减少对保护性共生菌群的破坏。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岁费城儿童的横断面研究中已有的数据。在2009- 2010年冬季呼吸道病毒流行季节收集样本和数据。高通量454 16S rRNA基因焦磷酸测序将用于表征鼻腔微生物群落。Illumina Genome Analyzer 2平台上的rna测序（RNA-seq）将用于在一系列实验条件下比较肺炎链球菌的转录谱。我们的具体目标是：1)在健康儿童、急性OM儿童和患有其他非细菌性上呼吸道感染的儿童的横断面样本中表征上呼吸道微生物群落结构，这些感染通常发生在急性OM发病之前；2)开发RNA- seq协议和生物信息学管道，以研究肺炎链球菌的转录谱，无论是单独的还是关键共生物种的存在。这些研究将确定参与肺炎链球菌定植和急性OM因果致病途径的正常菌群成员。新的方法将开发鉴定肺炎链球菌毒力基因独特表达在多微生物设置。从长远来看，这些数据将有助于益生菌等生物治疗药物的开发，也将为控制在呼吸道定植的其他细菌病原体提供相关信息。

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.