Highly multiplexed platforms for diagnosis of infection and immunity

快速、有效的鉴别诊断对于控制急性传染病的发病率和死亡率以及实现有效的资源分配至关重要。许多传染病都有非特异性的症状和体征；因此，仅有病史和体检通常不足以为临床治疗提供信息或确定暴发的特征。为了直接检测临床材料中的微生物核酸，已经开发了一系列广泛的分子方法。这些进展改变了微生物学和医学；尽管如此，这些方法中最高度多元化的高通量测序仍然过于复杂和昂贵，无法在许多临床环境中应用。此外，这些方法都不适用于可获取的样本中不存在微生物核酸的情况，或者疾病可能是由不再存在的病原体引发的情况。接触感染剂后发病的风险及其严重程度受个人以前接触过类似的感染剂或疫苗的影响。这种暴露可能提供完全或部分保护，或由于抗体介导的增强而导致更严重疾病的风险增加，就像登革热的情况一样。因此，了解一个人的免疫史可能会影响他/她的治疗、接种疫苗或在遇到特定病原体的可能性更高的地区作为急救人员或卫生保健工作者进行部署的决定。我们的目标是通过追求以下两个目标来加强传染病的鉴别诊断和管理：(1)建立一个新的高度多元化的血清学平台，用于描述受试者的病原体暴露史；(2)提高直接检测临床标本中微生物核酸的测序效率。对测序的投资主要集中在降低每个碱基的成本以及增加阅读长度和数量上。我们将通过建立新的样品制备方法来补充这些努力，这些方法将丰富相关模板，从而提高效率并降低生物信息学分析的复杂性。

Rapid, efficient differential diagnosis is critical to controlling the morbidity and mortality of acute infectious diseases and to enabling efficient resource allocation. Many infectious diseases present with non-specific signs and symptoms; hence, history and physical exam alone are typically insufficient to inform clinical management or characterize outbreaks. A wide range of molecular methods have been developed for direct detection of microbial nucleic acids in clinical materials. These advances have transformed microbiology and medicine; nonetheless, high throughput sequencing, the most highly multiplexed of these methods, remains too complex and expensive for application in many clinical settings. Furthermore, none of these methods will serve in instances where microbial nucleic acids are not present in an accessible sample or where disease may have been triggered by an agent that is no longer present. The risk of developing disease and its severity after exposure to an infectious agent is modulated by an individual's previous exposures to similar agents or vaccines. Such exposures may confer complete or partial protection or result in increased risk for more severe disease due to antibody-mediated enhancement, as is the case in dengue fever. Thus, knowledge of an individual's immunological history may influence decisions concerning his/her treatment, vaccination or deployment as a first responder or health care worker in areas with increased probability of encountering specific pathogens. Our objective is to enhance differential diagnosis and management of infectious diseases through pursuit of two aims that will (1) establish a new highly multiplexed serology platform for profiling a subject's pathogen exposure history and (2) improve the efficiency of sequencing for direct detection of microbial nucleic acids in clinical specimens. Investments in sequencing have largely focused on driving down costs per base and on increasing read length and number. We will complement these efforts by establishing new methods for sample preparation that will enrich for relevant template, thereby enhancing efficiency and reducing the complexity of bioinformatic analyses.