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

基本信息

批准号：
7890609
负责人：
Yousif Shamoo
金额：
$ 25.38万
依托单位：
RICE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-07-15 至 2013-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7890609
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 public health relevance resistance mechanism resistant strain transmission process vector

项目摘要

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）：CDC 估计，每年大约有 200 万例医院感染病例，导致 80,000 多名患者死亡。抗生素耐药性是成功药物治疗的进化结果，凸显了自然选择在形成导致耐药性的分子机制中的作用。为了从分子细节上研究这些机制，我们正在对大量携带三种抗生素抗性基因之一的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，由靶基因变化介导的抗生素抗性将用于：1）识别突变网络，这些突变网络定义了群体内适应的功能中间体； 2）确定导致适应性增加（即抗性）的蛋白质功能变化的物理化学基础，3）使用相关符号上位模型为成功进化轨迹的成功建模提供数据。研究的目标基因是粪肠球菌 Tn916 tetM（针对四环素的核糖体保护）、拟杆菌 Tn4400 tetX（四环素的酶促灭活）和 TnA TEM-1（（β-内酰胺）的酶促灭活）。这些研究将提供广泛的数据结果包括：拟杆菌 Tn4400 TetX 的高分辨率晶体结构和E. faecalis Tn916 TetM、用于药物开发的特征性扩展谱 TetX 和 TetM 突变体库、可扩展的高通量 TetM 活性测定以及用于持续进化的稳健的恒浊器系统的开发通过采取结合生物物理和群体策略的跨学科方法，我们可以将原子水平上的蛋白质变化与其对环境中生物体的影响联系起来，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。认识到，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，以防止耐药性。公共卫生相关性：抗生素耐药性的上升是一个明显的健康威胁，需要立即持续关注。随着耐药细菌继续扩散到医院和社区，社会付出的代价是惊人的。 2004 年的数据显示，尽管医学界尽了最大努力，但 60% 以上的 ICU 患者中发现了耐甲氧西林金黄色葡萄球菌 (MRSA)，近 30% 的 ICU 患者中发现了耐万古霉素肠球菌 (VRE)，而 2017 年 ICU 患者中这一比例分别为 37% 和 14%。 1995年又继续上升。儿童和老人尤其容易受到伤害。不幸的是，社区相关 (CA) 的 MRSA 疫情也在增加，这表明耐药菌株正在进入学校和其他公共区域的更衣室。除了临床环境中的人际传播外，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。转座子、接合转座子和质粒等可移动遗传元件充当微生物种群之间的载体，可以将耐药性传播到农业或临床环境之外。因此，医院和农场可以充当耐药基因向普通社区转移的滋生地和储存库。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于科学家和临床医生来说都是一笔宝贵的财富。这项工作是分子进化从分析过去事件的追溯姿态转变为主动使用进化研究来预测耐药性、优化药物方案以及可能开发新试剂的重要一步。限制病原体适应直接应用于医学。