Improved understanding of TB transmission by accounting for within-host heterogeneity of M. tuberculosis: A population-based molecular epidemiology study in a high HIV prevalent setting

摘要 在结核病（TB）高发病率环境中，TB患者通常感染多种菌株 分枝结核复合征（Mtbc）。尽管这是已知的事实，但目前的结核病传播研究在很大程度上忽视了 宿主内Mtbc异质性。我们认为，考虑到宿主内Mtbc异质性， 抽样偏差，并大大提高对结核病在家庭和 社区聚会场所。例如，在结核病高发地区进行的结核病传播研究发现， 同一家庭中同时发生的大多数结核病例具有不匹配的分子 指纹这一发现得出结论，大多数家庭结核病病例是获得性的 在家庭之外。然而，这些研究都没有适当地解释宿主内 异质性，这可能导致家庭内Mtbc遗传簇的检测失败。在 此外，尽管进行了大量的结核病传播研究，但预测结核病传播的因素仍然很差 明白考虑宿主内Mtbc的异质性可以提高对病原体和宿主的检测 影响传播的相关因素。总之，提高对这些领域的理解可以带来更多的 准确识别传播网络和疾病热点，从而可以指导干预措施， 阻断结核病传播。此外，拟议的研究可能会引发实践的重大变化 通过评估宿主内Mtbc异质性对结核病传播的影响， 结核病传播推断。 拟议的研究将通过结合两种新方法来解决目前的知识差距 为了检测宿主内Mtbc异质性：1）我们将对早期Mtbc进行全基因组测序（WGS）， 原代培养物样品以检测异质性Mtbc菌株;以及2）我们将进行基于靶向扩增子的 对系统发育和抗性预测重要的150个遗传位点进行测序。我们将使用先进的 生物信息学方法来整合这些关于Mtbc异质性的数据来源。拟议的研究将 还利用基于社区的挨家挨户主动个案调查，以尽量减少抽样偏差。这些方法将 应用于实现2个具体目标：1）确定考虑宿主内异质性的影响， 在基于人群的结核病传播研究中推断结核分枝杆菌菌株; 2）更准确地确定 家庭结核病例中可归因于家庭内传播的比例， 一项前瞻性的家庭接触研究。我们还将确定预测个体的病原体和宿主因素， 和人口水平的传播。该项目将产生有关结核病传播的重要科学知识 以及影响传播的因素，研究结果将为防治结核病的有针对性的干预措施提供信息和指导 通过中断当地的传播网络来控制流行病。

ABSTRACT In high tuberculosis (TB) incidence settings, individuals with TB are often infected with multiple strains of M. tuberculosis complex (Mtbc). Despite this known fact, current TB transmission studies largely ignore within-host Mtbc heterogeneity. We believe that accounting for within-host Mtbc heterogeneity will reduce sampling bias and significantly improve the understanding of TB transmission dynamics in households and in community gathering places. For example, TB transmission studies in high TB incidence settings have found that the majority of TB cases occurring concurrently within the same household have non-matching molecular fingerprints. This finding has led to the conclusion that the majority of household TB cases were acquired outside of the household. However, none of those studies have appropriately accounted for within-host heterogeneity, which could have led to missed detection of Mtbc genetic clusters within the household. In addition, despite numerous TB transmission studies, factors that predict TB transmission remain poorly understood. Accounting for within-host Mtbc heterogeneity could improve the detection of pathogen and host related factors that affect transmission. Together, improved understanding of these areas could lead to more accurate identification of transmission networks and disease hotspots, which can then guide interventions to interrupt TB transmission. Moreover, the proposed research could instigate significant changes in the practice of future TB transmission studies by evaluating the impact of accounting for within-host Mtbc heterogeneity on TB transmission inference. The proposed research will address the current gaps in knowledge by incorporating two novel methods for detecting within-host Mtbc heterogeneity: 1) we will conduct whole-genome sequencing (WGS) on early primary culture samples to detect heterogeneous Mtbc strains; and 2) we will perform targeted amplicon-based sequencing of 150 genetic loci important for phylogenetic and resistance prediction. We will use advanced bioinformatic methods to integrate these sources of data on Mtbc heterogeneity. The proposed research will also utilize community-based door-to-door active case finding to minimize sampling bias. These methods will be applied to achieve 2 specific aims: 1) to determine the impact of accounting for within-host heterogeneity of Mtbc strains on inference in a population-based TB transmission study; and 2) to determine more accurately the proportion of household TB cases that are attributable to transmission within the household by conducting a prospective household contact study. We will also determine pathogen and host factors that predict individual and population-level transmission. This project will generate important scientific knowledge of TB transmission and factors that affect transmission, and findings will inform and guide targeted interventions to combat TB epidemics by interrupting the transmission network in local settings.