Source Attribution and Transmission Dynamics of Campylobacter and Shigella Using Culture-Independent Molecular Methods in an Urban Slum in Dhaka, Bangladesh

虽然通过粪便-口腔接触暴露于肠道病原体的广泛途径是众所周知的，但我们对病原体特异性传播的理解存在严重局限性，特别是在低资源环境中的幼儿中。这种证据差距的一个关键原因是由于细菌培养的敏感性差而难以检测这些病原体，这对于志贺氏菌和弯曲杆菌来说尤其是一个问题。针对这些病原体的定量、非培养依赖性分子诊断的开发和应用大大改变了我们对人类疾病负担的理解，并准备为我们对这些病原体更广泛的生态学的理解做同样的事情。志贺氏菌和弯曲杆菌是研究传播生态学的模式生物，因为它们位于人与人（志贺氏菌）与环境（弯曲杆菌）传播连续体的两端。将两者纳入本项目提供了一系列可能的传播途径，从中我们可以推进对肠道病原体传播的理解。因此，本提案的目的是了解孟加拉国达卡城市低资源环境中肠道病原体的来源和传播途径，使用非培养检测方法。我们将通过使用系统动态建模方法来分析在家庭水平的纵向研究中产生的病原体检测数据来实现这一目标。传播队列将包括结构化观察，以量化人类与环境的接触，并对家庭接触者、动物宿主和环境进行广泛抽样，以确定和归属指数感染的来源。活力PCR将用于区分核酸和活生物体，这将使我们能够直接测量疾病后传播性病原体脱落的持续时间，并建立定量阈值，用于从广泛的样本中推断活病原体。然后，这些数据将被用来参数化两个互补的数学模型，一个家庭动态和地方病发病率模型，询问人与人之间和环境传播途径的相互依赖性和相对重要性。病原体将使用来自粪便和环境样品子集的短读段和长读段宏基因组测序的杂交组装在基因组水平上表征。该项目将改变我们对肠道病原体传播的理解，从对粪-口传播途径的广泛理解转向对病原体特异性的家庭和环境途径的最高相关性。在地方性和城市环境中，直接家庭接触与环境污染对志贺氏菌和弯曲杆菌传播的相对重要性是未知的，我们的建模方法将结合这些模型病原体在这个连续体上的位置。

While the broad routes of exposure to enteric pathogens through fecal-oral contact are well-known, there are critical limitations to our understanding of pathogen-specific transmission, especially in young children in low-resource settings. A key reason for this evidence gap is the difficulty in detecting these pathogens due to the poor sensitivity of bacterial culture, which is particularly a problem for Shigella and Campylobacter. The development and application of quantitative, culture-independent molecular diagnostics for these pathogens has substantially revised our understanding of the human burden of disease and is poised to do the same for our understanding of the broader ecology of these pathogens. Shigella and Campylobacter are model organisms to interrogate transmission ecology because they lie on opposite ends of the continuum of person-to-person (Shigella) versus environmental (Campylobacter) transmission. The inclusion of both in this project provides a range of likely transmission pathways from which we can advance our understanding of enteric pathogen transmission. The objective of this proposal is therefore to understand the sources and routes of transmission of enteric pathogens in an urban low-resource setting in Dhaka, Bangladesh using culture-independent methods for detection. We will accomplish this by using a systems-dynamic modeling approach to analyze pathogen detection data generated in a household-level longitudinal study. The transmission cohort will include structured observations to quantify human contacts with the environment and broad sampling of household contacts, animal reservoirs, and the environment to identify and attribute sources for index infections. Viability PCR will be used to differentiate nucleic acid from viable organisms, which will allow us to directly measure the duration of shedding of transmissible pathogen after illness and establish quantitative thresholds for inferring viable pathogen from a wide range of samples. These data will then be used to parameterize two complementary mathematical models, a household dynamics and endemic incidence model, to interrogate the interdependence and relative importance of person-to-person and environmental transmission pathways. Pathogens will be characterized to the genome level using hybrid assembly from short- and long-read metagenomic sequencing of a subset of stool and environmental samples. This project will transform our understanding of enteric pathogen transmission by moving from a broad understanding of fecal-oral transmission routes to pathogen-specific household and environmental pathways of highest relevance. In endemic and urban settings, the relative importance of direct household contact versus environmental contamination for transmission of both Shigella and Campylobacter is unknown, and our modeling approach will contextualize where these model pathogens lie on this continuum.