Comprehensive genetic characterization of antibiotic resistance

抗生素耐药性的综合遗传特征

• 批准号: 8493976
• 负责人: Saeed F Tavazoie
• 金额: $ 36.7万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2015-06-14
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8493976
• 关键词: Antibiotic Resistance; Antibiotics; Architecture; Bacterial Genome; Behavior; Binding Sites; Chemotaxis; Communities; Complex; Computing Methodologies; Development; Ecology; Elements; Escherichia coli; Genes; Genetic; Genetic Epistasis; Genome; Goals; Gram-Negative Bacteria; Health; Human; Intervention; Lead; Libraries; Medical; Pathway interactions; Pharmaceutical Preparations; Phenotype; Physiology; Play; Research; Resistance; Role; Second Messenger Systems; Sigma Factor; Signal Pathway; Technology; Time; Work; base; cell motility; combat; fight against; fitness; genome-wide; interest; knowledge of results; mutant; novel; public health relevance; technology development; trait

DESCRIPTION (provided by applicant): We propose to develop and apply a comprehensive set of experimental and computational methods for revealing the genetic basis of antibiotic tolerance in Escherichia coli. At the core of our approach is a microarray-based genetic footprinting technology that provides a global quantitative assessment of how each and every gene in the genome contributes to survival under antibiotic exposure. The identified genes will be placed within the context of genetic and regulatory networks through the application of a novel genome-wide epistasis analysis framework. We aim to explore both mild resistance to sub-lethal antibiotic exposure and severe tolerance as expressed in the context of 'persistence'. Preliminary studies provide strong proof-of-principle evidence for the framework we propose. Application of our approach to E. coli chemotaxis identifies 95% of known loci on the time-scale of weeks, reveals the organization of these loci into functional sub-modules, and identifies signaling pathways that regulate the context-dependent expression of motility. Furthermore, in a phenotype that has been extensively explored for over thirty year, we find three dozen additional novel loci that contribute through diverse mechanisms including the Rcs signaling pathway and cyclic-di-GMP second messenger system. The application of our approach to mild and lethal antibiotic exposure has already revealed more than a dozen loci whose genetic perturbations dramatically increase antibiotic tolerance. The proposed work promises to significantly expand the number of genes involved, and through the adjunct use of epistasis, co-expression, and co-inheritance analysis, allow us to place these genes within the context of genetic and regulatory networks. We expect our findings to fundamentally advance the understanding of antibiotic resistance and to provide the biomedical community with well-characterized pathways that serve as the basis for the development of new drugs.

描述（由申请人提供）：我们建议开发和应用一组全面的实验和计算方法，以揭示大肠杆菌中抗生素耐受性的遗传基础。我们方法的核心是一种基于微阵列的遗传足迹技术，该技术对基因组中的每个基因在抗生素暴露下如何有助于生存，从而提供全球定量评估。确定的基因将通过应用新型全基因组上学分析框架的应用，将其放置在遗传和调节网络的背景下。我们旨在探索在“持久性”背景下表达的轻度抗致命抗生素暴露和严重耐受性。初步研究为我们提出的框架提供了有力的原始证据。我们在大肠杆菌趋化性上的应用在数周的时间尺度上鉴定了95％的已知基因座，揭示了这些基因座的组织为功能子模块，并确定了调节背景依赖性运动表达的信号传导途径。此外，在经过30多年的广泛探索的表型中，我们发现了三个额外的新型基因座，这些基因座通过包括RCS信号途径和环状DI-GMP第二信使系统在内的各种机制做出了贡献。我们的方法在轻度和致命的抗生素暴露中的应用已经显示出了十几个基因座，其遗传扰动大大提高了抗生素耐受性。拟议的工作有望显着扩大所涉及的基因数量，并通过辅助使用，共同表达和共同传播分析，使我们能够将这些基因放置在遗传和调节网络的背景下。我们希望我们的发现从根本上提高人们对抗生素耐药性的理解，并为生物医学界提供充分的特征途径，作为开发新药的基础。