Defining evolutionary trajectories: Molecular adaptation to antibiotic resistance

定义进化轨迹：抗生素耐药性的分子适应

• 批准号: 8298634
• 负责人: Yousif Shamoo
• 金额: $ 28.8万
• 依托单位: RICE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8298634
• 关键词: Agriculture; Antibiotic Resistance; Antibiotics; Aquaculture; Area; Attention; Bacteria; Bacteroides; Biological Models; Breeding; Cefotaxime; Centers for Disease Control and Prevention (U.S.); Cessation of life; Characteristics; Child; Clinical; Communities; Community Hospitals; DNA Sequence; Data; Development; Disease Outbreaks; Drug Delivery Systems; Drug resistance; Elderly; Enterococcus faecalis; Environment; Enzymes; Escherichia coli; Event; Evolution; Family; Farming environment; Gene Targeting; General Practitioners; Genes; Genetic Epistasis; Grant; Health; Hospitals; Human; Lactams; Lead; Libraries; Link; Measurement; Mediating; Medical; Medicine; Methicillin; Mobile Genetic Elements; Modeling; Molecular; Molecular Evolution; Molecular Models; Mutation; Natural Selections; Nosocomial Infections; Organism; Pathway interactions; Patients; Pharmaceutical Preparations; Pharmacotherapy; Phenotype; Plasmids; Population; Population Dynamics; Population Pressures; Posture; Process; Property; Proteins; Reagent; Regimen; Research; Resistance; Resolution; Roentgen Rays; Role; Schools; Scientist; Societies; Specialist; Staphylococcus aureus; Structure; System; Testing; Tetracycline Resistance; Tetracyclines; Validation; Vancomycin resistant enterococcus; Work; assay development; base; clinically relevant; cost; direct application; drug development; drug resistant bacteria; experience; fitness; interdisciplinary approach; microbial; molecular modeling; molecular shape; mutant; novel; prevent; protein function; protein structure function; resistance mechanism; resistant strain; transmission process; vector

DESCRIPTION (provided by applicant): Each year the CDC estimates that there are approximately two million cases of nosocomial infection that result in over 80,000 patient deaths. Antibiotic resistance is an evolutionary consequence of successful drug therapies and highlights the role of natural selection in shaping the molecular mechanisms leading to resistance. To examine these mechanisms in molecular detail, we are subjecting large populations of bacteria, carrying one of three antibiotic resistance genes, to continuous experimental evolution. By varying the conditions of selection during adaptation, antibiotic resistance mediated by changes to the target genes will be used to: 1) identify the network of mutations that define the functional intermediates to adaptation within the population; 2) determine the physicochemical basis for changes in protein function that lead to increased fitness (i.e. resistance) and 3) provide data for the successful modeling of successful evolutionary trajectories using correlated sign epistasis models. The target genes for study are E. faecalis Tn916 tetM (ribosomal protection against tetracyclines), Bacteroides Tn4400 tetX (enzymatic inactivation of tetracyclines) and TnA TEM-1 (enzymatic inactivation of (-lactams). These studies will provide a wide range of data and results including: high resolution crystallographic structures of Bacteroides Tn4400 TetX and E. faecalis Tn916 TetM, libraries of characterized expanded spectrum TetX and TetM mutants for drug development, a scalable high throughput TetM activity assay, and development of robust turbidostat systems for continuous evolution. By taking an interdisciplinary approach combining biophysical and population strategies, we can link changes in proteins at the atomic level to their consequences for the organism in its environment and vice versa. Developing validated models for molecular adaptation is an important step towards making accurate predictions of antibiotic resistance. Once fully realized, evolutionary forecasting holds the promise of going beyond the identification of traditional drug targets to the development of new clinical strategies that consider the molecular mechanisms of adaptation to prevent drug resistance. PUBLIC HEALTH RELEVANCE: The rise of antibiotic resistance is a clear health threat that requires immediate and continuing attention. As strains of drug resistant bacteria continue to spread into hospitals and communities the cost to society are staggering. Data from 2004 show that despite the best efforts of the medical community, methicillin resisistant Staphylococcus aureus (MRSA) were found in over 60% and vancomycin resistant Enterococci (VRE) in nearly 30% of ICU patients compared to 37% and 14% respectively in 1995 and continue to rise. Children and the elderly are particularly vulnerable. Unfortunately, community associated (CA) outbreaks of MRSA are also increasing suggesting that drug resistant strains are making their way into the locker rooms of schools and other public areas. In addition to human-to-human transmission within clinical settings, the widespread use of antibiotics in agriculture and aquaculture has also led to the proliferation of resistant strains. Mobile genetic elements such as transposons, conjugative transposons and plasmids act as vectors between microbial populations and can spread resistance beyond the agricultural or clinical environment. Hospitals and farms can therefore act as breeding grounds and reservoirs for the transfer of drug resistance genes into the general community. Although there is no way to stop evolution, a more complete understanding of the principles underlying molecular adaptation to resistance can be a powerful asset to both scientists and clinicians. The proposed work is an important step in the transition of molecular evolution from a retroactive posture that analyzes past events to one in which evolution research is used pro-actively for the prediction of drug resistance, optimization of drug regimens, and perhaps development of novel reagents that restrict pathogenic adaptation with direct application to medicine.

描述(由申请人提供)：美国疾病控制与预防中心估计，每年大约有200万例医院感染病例，导致超过80,000名患者死亡。抗生素耐药性是成功的药物治疗的进化结果，并突显了自然选择在形成导致耐药性的分子机制方面的作用。为了从分子上详细研究这些机制，我们让携带三种抗生素耐药基因之一的大量细菌进行持续的实验进化。通过改变适应过程中的选择条件，通过改变目标基因介导的抗生素耐药性将被用于：1)确定定义群体内适应的功能中间产物的突变网络；2)确定导致适应度增加的蛋白质功能变化的物理化学基础；以及3)为使用相关的符号上位模型成功地模拟成功的进化轨迹提供数据。研究的目标基因是粪肠球菌Tn916(对四环素的核糖体保护)、类杆菌Tn4400(四环素的酶失活)和TNA TEM-1(对内酰胺类抗生素的酶失活)。这些研究将提供广泛的数据和结果，包括：类杆菌Tn4400 TetX和粪类杆菌Tn916 TetM的高分辨率晶体结构，用于药物开发的特征扩展光谱TetX和TetM突变体文库，可扩展的高通量TetM活性测定，以及用于持续进化的强大的浊度测定系统的开发。通过采取结合生物物理学和种群策略的跨学科方法，我们可以将蛋白质在原子水平上的变化与其对有机体环境的影响联系起来，反之亦然。开发经过验证的分子适应模型是准确预测抗生素耐药性的重要一步。一旦完全实现，进化预测有望超越传统药物靶点的识别，发展新的临床策略，考虑适应的分子机制来防止耐药性。与公共卫生相关：抗生素耐药性的上升是一个明显的健康威胁，需要立即和持续关注。随着耐药细菌菌株继续传播到医院和社区，给社会带来的成本是惊人的。2004年的数据显示，尽管医学界做出了最大的努力，但在ICU患者中，甲氧西林耐药金黄色葡萄球菌(MRSA)和万古霉素耐药肠球菌(VRE)的比例分别超过60%和近30%，而1995年分别为37%和14%，而且还在继续上升。儿童和老年人尤其容易受到伤害。不幸的是，社区相关(CA)MRSA的爆发也在增加，这表明耐药菌株正在进入学校和其他公共场所的更衣室。除了在临床环境中人与人之间的传播外，抗生素在农业和水产养殖中的广泛使用也导致了耐药菌株的扩散。可移动的遗传元件，如转座子、接合转座子和质粒，作为微生物种群之间的媒介，可以将耐药性传播到农业或临床环境之外。因此，医院和农场可以成为将抗药性基因转移到普通社区的滋生地和蓄水池。尽管没有办法阻止进化，但更全面地了解分子适应耐药性的原理对科学家和临床医生来说都是一项强大的财富。这项拟议的工作是分子进化从分析过去事件的追溯状态过渡到主动使用进化研究预测耐药性、优化药物方案，也许还会开发限制病原适应的新试剂直接应用于医学的重要一步。