ESTABLISHMENT AND DYNAMICS OF ANTIBIOTIC RESISTANCE RESERVOIRS IN DEVELOPING INTE

描述(申请人提供)：近几十年来，耐多药细菌病原体的流行急剧增加，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)，使病原体能够迅速对抗生素治疗不敏感。因此，有必要系统地描述病原菌可获得的许多抗生素耐药基因(或‘抗药性’)的遗传储存库。由于(1)共生体和病原体之间容易接触和遗传交换，(2)用基于文化的方法对该群落进行采样，以及(3)早期人类生活中群落组成的动态特性，人类肠道微生物区系具有特别重要的研究价值。我们建议使用一种强大的、独立于文化的功能元基因组选择与下一代测序的组合来深入表征生命的头两年肠道耐药组的发育。我们寻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剂的组装和动态。其次，我们将了解耐药组的动员潜力(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检验抗生素暴露、出生后年龄以及共同的环境和宿主遗传学驱动肠道耐药组的丰富性、多样性和传播的假说，来表征健康婴儿的抵抗体发育。我们的第二个目标是通过测试以下假设来了解极低出生体重(VLBW)婴儿的病理耐药发展：抗生素治疗的频谱和持续时间决定了这些典型的低多样性微生物群中肠道耐药菌的丰度、多样性和传播。在这两个目标中，我们将重点关注发展中的微生物群落中抗性基因的多样性、丰度和遗传背景。我们将从三个重要方面加强对寄主相关微生物群落动力学的基本了解：(1)阐明在婴儿出生后头两年纵向采样的肠道微生物区系发育过程中抵抗器的组装和动力学；(2)确定基因交换在微生物发育中的作用 使用抗生素耐药性和相关的可移动遗传元素作为临床相关和易于检测的微生物群落功能的微生物群落，以及(3)应用元基因组学、下一代测序和计算生物学的技术创新，显著提高产量和降低微生物群落功能研究的成本。我们研究的潜在影响是：(1)开发一种新的框架，用于经济、高通量地表征微生物群落的功能；(2)为未来的工作提供基础，以减少因不适当的措施而导致的新生儿发病率和死亡率。 肠道微生物区系的定植动态，以及(3)为更谨慎地使用抗生素建立翻译证据库。

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.