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套全面的实验和计算方法来揭示大肠杆菌抗生素耐受性的遗传基础。我们方法的核心是基于微阵列的基因足迹技术，该技术可以对基因组中的每个基因如何在抗生素暴露下促进生存提供全球定量评估。通过应用新型全基因组上位性分析框架，所识别的基因将被置于遗传和调控网络的背景下。我们的目标是探索对亚致死抗生素暴露的轻度耐药性和“持久性”中所表达的严重耐受性。初步研究为我们提出的框架提供了强有力的原理证明证据。应用我们的大肠杆菌趋化性方法，可以在数周的时间范围内识别出 95% 的已知基因座，揭示这些基因座组织成功能子模块的方式，并识别调节运动的上下文依赖性表达的信号通路。此外，在已经广泛探索了三十多年的表型中，我们发现了三打额外的新位点，它们通过不同的机制发挥作用，包括 Rcs 信号通路和环二 GMP 第二信使系统。我们对轻度和致命抗生素暴露的方法的应用已经揭示了十多个位点，其遗传扰动显着增加了抗生素耐受性。拟议的工作有望显着扩大所涉及基因的数量，并通过辅助使用上位性、共表达和共继承分析，使我们能够将这些基因置于遗传和调控网络的背景下。我们希望我们的研究结果能够从根本上增进对抗生素耐药性的理解，并为生物医学界提供明确的途径，作为新药开发的基础。