ESTABLISHMENT AND DYNAMICS OF ANTIBIOTIC RESISTANCE RESERVOIRS IN DEVELOPING INTE

描述（由申请人提供）：近几十年来，多重耐药细菌病原体的流行率急剧增加，威胁着我们治疗感染的能力。虽然病原体可能通过个别突变产生抗生素耐药性，但获得耐药性的最常见手段是通过水平基因转移（HGT），使病原体能够迅速发展对抗生素治疗不敏感。因此，有必要系统地表征病原体可获得的抗生素抗性基因（或“抗性基因”）的许多遗传库。人类肠道微生物群具有特别重要的耐药基因组，这是由于（1）细菌和病原体之间容易接触和遗传交换，（2）基于培养的方法对该群落的历史采样不足，以及（3）人类早期生活中群落组成的动态特性。我们建议使用功能宏基因组学选择与下一代测序的强大的、不依赖于培养的组合来深入表征生命的前两年中肠耐药基因组的发展。 我们力求实现两个首要目标。首先，我们将定义遗传和环境因素（包括抗生素治疗）如何影响婴儿肠道抵抗体的组装和动力学。其次，我们将了解如何动员的抗性基因组（定义为关联的抗性基因与移动的遗传因素）的潜力影响这个关键的生态系统的稳定性。为此，我们的第一个具体目标是通过测试以下假设来表征健康婴儿中的耐药基因组发育：抗生素暴露、出生后年龄、共享环境和宿主遗传学驱动肠道耐药基因组的丰度、多样性和传播。我们的第二个目的是通过测试以下假设来了解极低出生体重（VLBW）婴儿的病理性耐药组发展：抗生素治疗的范围和持续时间驱动这些特征性低多样性微生物中肠道耐药组的丰度、多样性和传播。在这两个目标中，我们将关注发展中微生物群落中抗性基因的多样性、丰度和遗传背景。 我们将通过三种重要方式加强对宿主相关微生物群落动态的基本理解：（1）阐明在生命最初两年纵向采样的婴儿肠道微生物群发育中耐药基因组的组装和动态，（2）确定遗传交换在微生物群落发育中的作用，（3）确定在肠道微生物群发育中的作用。 利用抗生素耐药性和相关的移动的遗传元件作为临床相关和易于测定的微生物群落功能，以及（3）应用宏基因组学、下一代测序和计算生物学中的技术创新，以显著增加通量并降低研究微生物群落功能的成本。我们的研究的潜在影响是：（1）开发一个新的框架，用于经济，高通量表征微生物群落功能，（2）为未来的工作提供基础，以减轻由于不适当的微生物引起的新生儿期婴儿发病率和死亡率。 肠道微生物群的定殖动力学，以及（3）建立更谨慎使用抗生素的转化证据基础。

DESCRIPTION (provided by applicant): The prevalence of multi-drug resistant bacterial pathogens has increased dramatically in recent decades, threatening our ability to treat infections. Though pathogens may develop antibiotic resistance through individual mutations, the most common means of acquiring resistance is through horizontal gene transfer (HGT), enabling pathogens to rapidly develop insensitivity to antibiotic therapy. Therefore, it is essentil to systematically characterize the many genetic reservoirs of antibiotic resistance genes (or 'resistomes') accessible to pathogens. The human gut microbiota harbor a particularly important resistome to study due to (1) easy contact and genetic exchange between commensals and pathogens, (2) historic under sampling of this community with culture-based approaches, and (3) the dynamic properties of community composition in early human life. We propose to deeply characterize the development of the intestinal resistome in the first two years of life using a powerful, culture- independent combination of functional metagenomics selections with next-generation sequencing. We seek to achieve two overarching goals. First, we will define how genetic and environmental factors (including antibiotic treatment) affect the assembly and dynamics of the infant gut resistome. Second, we will understand how the potential for mobilization of the resistome (defined by association of resistance genes with mobile genetic elements) influence the stability of this critical ecosystem. To this end, our first specific aim i to characterize resistome development in healthy infants through testing the hypothesis that antibiotic exposure, postnatal age, and shared environment and host genetics drive the abundance, diversity and dissemination of gut resistomes. Our second aim is to understand pathologic resistome development of very-low birth weight (VLBW) infants by testing the hypothesis that spectrum and duration of antibiotic therapy drive the abundance, diversity, and dissemination of the gut resistome in these characteristically low-diversity microbiotas. In both aims, we will focus on diversity, abundance, and genetic context of resistance genes in the developing microbial community. We will enhance fundamental understanding of host-associated microbial community dynamics in three significant ways: (1) Illuminating assembly and dynamics of the resistome in developing gut microbiota of infants sampled longitudinally over the first two years of life, (2) defining the role of genetic exchange in developing microbial communities using antibiotic resistance and associated mobile genetic elements as clinically-relevant and easily-assayed microbial community functions, and (3) applying technological innovations in metagenomics, next-generation sequencing, and computational biology to dramatically increase throughput and decrease costs of studying microbial community functions. Potential impacts of our study are: (1) developing a novel framework for economical, high-throughput characterization of microbial community functions, (2) providing a basis for future work to mitigate infant morbidity and mortality in the neonatal period resulting from inappropriate colonization dynamics of gut microbiota, and (3) establishing a translational evidence base for more prudent use of antibiotics.