School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA.
Appl Environ Microbiol. 2019 Nov 27;85(24). doi: 10.1128/AEM.01820-19. Print 2019 Dec 15.
is a leading contributor to infectious diarrhea and child mortality worldwide, but it remains unknown how alterations in the gut microbiome vary for distinct pathotype infections and whether these signatures can be used for diagnostic purposes. Further, the majority of enteric diarrheal infections are not diagnosed with respect to their etiological agent(s) due to technical challenges. To address these issues, we devised a novel approach that combined traditional, isolate-based and molecular-biology techniques with metagenomics analysis of stool samples and epidemiological data. Application of this pipeline to children enrolled in a case-control study of diarrhea in Ecuador showed that, in about half of the cases where an pathotype was detected by culture and PCR, was likely not the causative agent based on the metagenome-derived low relative abundance, the level of clonality, and/or the virulence gene content. Our results also showed that diffuse adherent (DAEC), a pathotype that is generally underrepresented in previous studies of diarrhea and thus, thought not to be highly virulent, caused several small-scale diarrheal outbreaks across a rural to urban gradient in Ecuador. DAEC infections were uniquely accompanied by coelution of large amounts of human DNA and conferred significant shifts in the gut microbiome composition relative to controls or infections caused by other pathotypes. Our study shows that diarrheal infections can be efficiently diagnosed for their etiological agent and categorized based on their effects on the gut microbiome using metagenomic tools, which opens new possibilities for diagnostics and treatment. infectious diarrhea is an important contributor to child mortality worldwide. However, diagnosing and thus treating infections remain challenging due to technical and other reasons associated with the limitations of the traditional culture-based techniques and the requirement to apply Koch's postulates. In this study, we integrated traditional microbiology techniques with metagenomics and epidemiological data in order to identify cases of diarrhea where was most likely the causative disease agent and evaluate specific signatures in the disease-state gut microbiome that distinguish between diffuse adherent, enterotoxigenic, and enteropathogenic pathotypes. Therefore, our methodology and results should be highly relevant for diagnosing and treating diarrheal infections and have important applications in public health.
是导致全球传染性腹泻和儿童死亡的主要原因之一，但目前尚不清楚肠道微生物组的改变如何因不同的血清型感染而有所不同，以及这些特征是否可用于诊断目的。此外，由于技术挑战，大多数肠源性腹泻感染并未根据其病因（病原体）进行诊断。为了解决这些问题，我们设计了一种新方法，将传统的、基于分离物的和分子生物学技术与粪便样本的宏基因组分析以及流行病学数据相结合。将该方法应用于厄瓜多尔腹泻病例对照研究中招募的儿童，结果表明，在通过培养和 PCR 检测到血清型的病例中，约有一半情况下，基于宏基因组衍生的相对丰度低、克隆水平和/或毒力基因含量，可能不是致病因子。我们的研究结果还表明，普遍认为毒力不高的弥漫性粘附性（DAEC）血清型在以前的腹泻研究中代表性不足，因此不会引起高腹泻发病率，但在厄瓜多尔从农村到城市的梯度上，引起了几次小规模腹泻暴发。DAEC 感染独特地伴随着大量人类 DNA 的共洗脱，并与对照组或由其他血清型引起的感染相比，显著改变了肠道微生物组的组成。我们的研究表明，使用宏基因组工具可以有效地针对病因诊断腹泻感染，并根据其对肠道微生物组的影响进行分类，这为诊断和治疗开辟了新的可能性。传染性腹泻是导致全球儿童死亡的重要原因之一。然而，由于与传统基于培养的技术的局限性和科赫假设的应用相关的技术和其他原因，诊断和治疗变得具有挑战性。在这项研究中，我们整合了传统微生物学技术与宏基因组学和流行病学数据，以确定最有可能是腹泻致病因子的病例，并评估疾病状态肠道微生物组中的特定特征，这些特征可区分弥漫性粘附性、肠毒性和肠致病性血清型。因此，我们的方法和结果对于诊断和治疗腹泻感染应该具有重要意义，并在公共卫生方面具有重要应用。
