Antimicrobial Resistance and Horizontal Gene Transfer in the Human Gut Microbiome in Response to an Antibiotic

人类肠道微生物组对抗生素的耐药性和水平基因转移

基本信息

批准号：
10176389
负责人：
DAVID A. RELMAN
金额：
$ 72.61万
依托单位：
PALO ALTO VETERANS INSTIT FOR RESEARCH
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-06-01 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10176389
关键词：
Address Adult Affect Anaerobic Bacteria Antibiotics Antimicrobial Resistance Bacteriophages Biological Assay Ciprofloxacin Communicable Diseases Communities Complex Data Development Elements Environment Event Evolution Exposure to Feces Genes Genetic Genome Genomics Goals Horizontal Gene Transfer Human In Vitro Individual Infection Knowledge Laboratories Link Metagenomics Methods Microbe Mobile Genetic Elements Modernization Monitor Pathogenicity Plasmids Prevalence Protocols documentation Recording of previous events Resistance development Resolution Sampling Source Work antimicrobial chromosome conformation capture de novo mutation emerging antimicrobial resistance gut microbiome gut microbiota improved in vivo innovation metagenomic sequencing microbial community microbial genome microbial host mortality pathogen preservation pressure resistance gene response stool sample temporal measurement tool trend

项目摘要

PROJECT SUMMARY Antimicrobial resistance (AMR) is an increasingly prevalent and serious problem worldwide. Most often, AMR arises from horizontal gene transfer (HGT), involving mobile genetic elements (MGE) such as plasmids and phages. The human gut is a hotspot for both the evolution and spread of AMR; commensals serve as a source of AMR for pathogens via HGT. Slowing the evolution and spread of AMR is both possible and necessary. Knowledge about the evolutionary history of AMR development and dissemination in vivo is essential to facilitate effective stewardship. Yet, this knowledge remains limited. Important aspects of AMR evolution become evident only in complex environments and in the setting of diverse communities. We will study responses to antibiotic exposure in the human gut microbiota in vivo, as well as in complex stool-derived subject-specific communities in vitro, at high temporal resolution and using innovative approaches. We will link AMR and other MGE- associated genes to their host core genomes using high throughput chromosome conformation capture (Hi-C) and monitor these genes and elements in bacterial hosts before, during and after antibiotic exposure. The short term-objectives of the proposed work are to characterize and assess the contributions of de novo mutations and HGT to the spread and development of AMR in the human gut microbiota during antibiotic exposure. The long- term objectives are to improve antibiotic stewardship by identifying critical events or transitions in the evolution and dissemination of AMR in vivo, and the factors and conditions that make those events less likely. Aim 1. Determine the distribution of antimicrobial resistance genes in the gut microbiota of healthy humans. We will use Hi-C and metagenomic sequencing to resolve strain-level microbial genomes from stool samples of 60 healthy adults collected over an 8-week antibiotic-free interval, prior to a ciprofloxacin exposure. We will identify potential AMR genes and determine their distribution within core and accessory genomes, and in association with mobile genetic elements. Aim 2. Characterize the effects of ciprofloxacin on the abundance and mobilization of AMR genes in the human gut microbiota in vivo. We will use Hi-C and metagenomic sequencing to assay stool samples collected from the same 60 subjects during and after the ciprofloxacin exposure, and to characterize the composition and dynamics of selective sweeps that affect the emergence of AMR. Aim 3. Characterize the effects of ciprofloxacin on the mobilization of AMR genes in synthetic, human gut-derived microbial communities in vitro. We will propagate pre-exposure fecal communities ex vivo from all 60 subjects, as well as generate complex, synthetic communities from pre-exposure samples of 5 subjects, and then passage both bulk and synthetic communities anaerobically under multiple ciprofloxacin regimes. We will identify factors and conditions that affect emergence of AMR through HGT and de novo mutations in vitro.

项目概要抗菌素耐药性（AMR）是世界范围内日益普遍和严重的问题。最常见的是， AMR 源自水平基因转移 (HGT)，涉及移动遗传元件 (MGE)，例如质粒和噬菌体。人类肠道是 AMR 进化和传播的热点；共生体充当通过 HGT 获得病原体 AMR 的来源。减缓抗微生物药物耐药性的演变和传播既是可能的，也是必要的。了解体内 AMR 发展和传播的进化史对于促进有效的管理。然而，这些知识仍然有限。 AMR 演变的重要方面变得显而易见只有在复杂的环境和不同的社区环境中。我们将研究对抗生素的反应暴露于体内人类肠道微生物群以及复杂的粪便衍生的受试者特定群落中在体外，以高时间分辨率并使用创新方法。我们将链接 AMR 和其他 MGE- 使用高通量染色体构象捕获 (Hi-C) 将基因与其宿主核心基因组相关联并在接触抗生素之前、期间和之后监测细菌宿主中的这些基因和元素。短的拟议工作的长期目标是描述和评估从头突变的贡献和 HGT 与抗生素暴露期间人类肠道微生物群中 AMR 的传播和发展有关。长- 术语目标是通过识别进化中的关键事件或转变来改善抗生素管理体内 AMR 的传播和传播，以及导致这些事件发生可能性较小的因素和条件。目标 1. 确定健康人肠道微生物群中抗菌素耐药性基因的分布人类。我们将使用 Hi-C 和宏基因组测序来解析粪便中的菌株水平微生物基因组在接触环丙沙星之前，在 8 周的无抗生素间隔期间收集了 60 名健康成年人的样本。我们将识别潜在的 AMR 基因并确定它们在核心和辅助基因组中的分布，以及与移动遗传元件相关。目标 2. 表征环丙沙星对 AMR 基因丰度和动员的影响人体内肠道微生物群。我们将使用 Hi-C 和宏基因组测序来分析收集的粪便样本来自相同的 60 名受试者在环丙沙星暴露期间和之后的数据，并表征其成分和影响 AMR 出现的选择性清除动态。目标 3. 表征环丙沙星对合成人类 AMR 基因动员的影响体外肠道来源的微生物群落。我们将在体外繁殖暴露前粪便群落所有 60 名受试者，以及从 5 名受试者的暴露前样本中生成复杂的合成群落，然后在多种环丙沙星方案下厌氧地传代散装群落和合成群落。我们将确定通过 HGT 和体外新生突变影响 AMR 出现的因素和条件。