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)高发环境中，结核病患者通常感染多种菌株。 结核分支杆菌复合体(MTBC)。尽管如此，目前的结核病传播研究在很大程度上忽略了 主机内MTBC异质性。我们相信，考虑到主机内MTBC的异构性将减少 抽样偏差和显著提高了对家庭和#年结核病传播动态的了解 社区聚集地。例如，在结核病高发环境中的结核病传播研究发现 在同一个家庭内同时发生的大多数结核病病例具有不匹配的分子 指纹。这一发现导致得出结论，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考虑到宿主内部的情况 异质性，这可能导致遗漏检测到家庭内的MTBC基因簇。在……里面 此外，尽管有许多结核病传播研究，但预测结核病传播的因素仍然很少。 明白了。考虑宿主内MTBC的异质性可以提高病原体和宿主的检测 影响传播的相关因素。总而言之，对这些领域的更好理解可能会带来更多 准确识别传播网络和疾病热点，从而指导干预措施 阻断结核病的传播。此外，拟议的研究可能会在实践中引发重大变化。 通过评估考虑宿主内MTBC异质性对未来结核病传播研究的影响 结核病传播推断。 拟议的研究将通过结合两种新的方法来解决目前的知识差距 为了检测宿主内MTBC的异质性：1)我们将在早期进行全基因组测序 原代培养样本以检测不同的MTBC菌株；以及2)我们将进行基于靶向扩增的 对系统发育和抗性预测具有重要意义的150个遗传基因座的测序。我们将使用高级 生物信息学方法整合这些关于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的活跃病例查找，以最大限度地减少抽样偏差。这些方法将 应用于实现2个具体目标：1)确定考虑主机内异质性的影响 结核分枝杆菌菌株在以人群为基础的结核病传播研究中的推断；以及2)更准确地确定 可归因于通过以下方式在家庭内传播的家庭结核病病例的比例 一项前瞻性家庭接触研究。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，这些发现将为抗击结核病的有针对性的干预提供信息和指导 通过中断当地的传输网络来传播流行病。

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.