ESTABLISHMENT AND DYNAMICS OF ANTIBIOTIC RESISTANCE RESERVOIRS IN DEVELOPING INTE

描述（由申请人提供）：近几十年来，耐多药细菌病原体的流行率急剧增加，威胁到我们治疗感染的能力。虽然病原体可能通过个体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），使病原体迅速对抗生素治疗不敏感。因此，有必要系统地描述病原体可获得的抗生素耐药基因（或“抗性组”）的许多遗传库。人类肠道微生物群拥有一个特别重要的抵抗组，因为(1)共生体和病原体之间容易接触和遗传交换，(2)以培养为基础的方法对该群落进行了历史性的采样，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选择与下一代测序相结合的强大，培养独立的组合来深入表征生命最初两年肠道抵抗组的发育。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组的组装和动态。其次，我们将了解抵抗组动员的潜力（由抗性基因与可移动遗传元件的关联定义）如何影响这一关键生态系统的稳定性。为此，我们的第一个具体目标是通过测试抗生素暴露、出生后年龄、共同环境和宿主遗传驱动肠道抗性组的丰度、多样性和传播的假设来表征健康婴儿的抗性组发育。我们的第二个目标是通过测试抗生素治疗的谱和持续时间驱动肠道抵抗组在这些特征低多样性微生物群中的丰度、多样性和传播的假设来了解极低出生体重（VLBW）婴儿的病理抵抗组发育。在这两个目标中，我们将关注发展中的微生物群落中耐药基因的多样性、丰度和遗传背景。我们将从三个重要方面加强对宿主相关微生物群落动态的基本理解：(1)阐明在出生后两年内纵向采样的婴儿肠道微生物群发育中抵抗组的组装和动力学，(2)定义遗传交换在微生物发育中的作用

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.