Microbial diversity, otitis media, and the pneumococcal transctiptome

描述(由申请人提供)：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。肺炎链球菌的定植是疾病过程中的一个关键步骤，发生在复杂的微生物群落中。对细菌定植模式和OM风险之间关系的有限了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结果，并最大限度地减少对保护性共生菌群的破坏。我们建议的研究是对NIDCD计划公告(PA-08-092)“研究多微生物疾病的新方法”的直接回应。我们将分析来自费城249名6个月至3岁儿童的横断面研究的预先存在的数据。样本和数据是在2009-10冬季呼吸道病毒季节收集的。高通量454个16S rRNA基因焦磷酸测序将用于表征鼻腔微生物群落。在Illumina Genome Analyzer 2平台上的RNA测序(RNA-seq)将用于比较肺炎链球菌在一系列实验条件下的转录图谱。我们的具体目标是：1)表征健康儿童、急性OM儿童和其他以非细菌性上呼吸道感染为主的儿童横断面样本中的上呼吸道微生物群落结构，这些感染通常是急性OM发病之前的；2)建立RNA-SEQ程序和生物信息学管道，以单独和在关键共生物种存在的情况下研究肺炎链球菌的转录图谱。这些研究将确定与肺炎链球菌定植和急性OM的致病途径有关的正常菌群成员。将开发新的方法来识别在多菌环境中唯一表达的肺炎链球菌毒力基因。从长远来看，这些数据将有助于益生菌等生物疗法的发展，还将提供与控制其他定居在呼吸道的细菌病原体有关的信息。 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风险和中耳炎之间的关系。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.