Determining the architecture of antibiotic resistance evolvability

确定抗生素耐药性进化的结构

基本信息

批准号：
BB/X007979/1
负责人：
Danna Gifford
金额：
$ 73.64万
依托单位：
University of Manchester
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2023
资助国家：
英国
起止时间：
2023 至无数据
项目状态：
未结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FX007979%2F1
关键词：
Determining architecture antibiotic resistance evolvability

项目摘要

The growing prevalence of antibiotic resistance is a major crisis for both public health and agriculture. Bacteria can dramatically vary in their ability to evolve resistance, but our ability to predict which ones will go on to evolve high-level resistance is currently limited. Understanding what contributes to the evolutionary potential for resistance will enable us to develop new interventions for suppressing antimicrobial resistance. It is therefore important to understand the genomic mechanisms that contribute to the 'evolvability' of resistance.We will investigate how genome diversity contributes to the ability to evolve resistance. In contrast to other work that focuses on a single species of bacteria, we will investigate how between-species genome diversity contributes to the ability to evolve resistance. We will focus on Pseudomonas bacteria, an incredibly diverse genus that includes environmental, commensal and pathogenic organisms. Pseudomonas imposes a global economic burden that exceeds £150 billion GBP annually across health and agricultural sectors. Antibiotic resistance in Pseudomonas is increasing rapidly, and understanding what allows resistance to evolve to important anti-pseudomonal antibiotics is key to maintaining the ability to manage Pseudomonas. We will therefore determine how genome-level variation contributes to the evolvability of resistance to anti-pseudomonal antibiotics, including one recently come to market specifically designed to target pseudomonad physiology (cefiderocol).Evidence from Pseudomonas suggests that even seemingly minor differences in genome content can have extensive consequences for the potential to evolve resistance. Previous work has shown that a single 'evolvability gene' can influence whether pseudomonads can evolve high-level resistance to the antibiotic ceftazidime. However, we currently do not know the extent to which such mechanisms generally operate. Specifically, little is known about (i) how resistance evolvability varies across diverse antibiotic classes, (ii) whether different evolvability mechanisms operate for single- and multi-drug resistance, and (iii) whether disrupting such genes can maintain or restore antibiotic sensitivity.To address these questions, we will use a multi-disciplinary approach called 'comparative experimental evolution', a powerful technique able to investigate how species-level differences in genome content affect the ability for bacteria to evolve resistance. This approach combines high-throughput experimental evolution and bacterial phenotyping with whole genome sequencing and comparative genomics. We will evolve nearly 60,000 independent populations from eight Pseudomonas species under single- and multiple-antibiotic environments. We will connect differences in genome content to differences in mutations acquired by each species that confer high-level resistance. We will then use modern genome editing techniques to see if disrupting evolvability genes can constrain resistance, or restore sensitivity in already-resistant organisms. These massively parallel experiments will reveal the genomic basis for resistance evolvability, while also revealing the connection between high-level resistance and chromosomal mutations. This project will advance our knowledge of what potentiates resistance evolution in these economically-important bacteria. It will also provide a framework from which we can identify genetic markers for predicting the risk of resistance evolution, allowing better targeted use of antimicrobials. Finally, it will provide a framework for testing anti-evolvability approaches to preventing resistance and restoring sensitivity.

抗生素抗性的越来越多是公共卫生和重新制定的重大危机。细菌的发展能力可能会大大变化，但是我们预测哪些将继续发展高级抗性的能力目前受到限制。了解有助于进化潜力的是什么将使我们能够制定新的干预措施来抑制抗菌抗性。因此，重要的是要了解有助于抗性的“可发展性”的基因组机制。我们将研究基因组多样性如何有助于发展抗性的能力。与其他侧重于单一种细菌的工作相反，我们将研究物种之间的基因组多样性如何有助于发展抗性的能力。我们将专注于假单胞菌细菌，这是一个越来越多样化的属，包括环境，共生和致病组织。假单胞菌不可能在健康和农业领域每年超过1500亿英镑的全球经济负担。假单胞菌中的抗生素耐药性正在迅速增加，并且了解允许抵抗力发展为重要抗假单胞菌抗生素的原因是维持管理假单胞菌的能力的关键。因此，我们将确定基因组水平的变异如何促进对抗毒素抗生素的抵抗力的演变，其中包括最近旨在靶向靶向假性假单胞菌生理学（Cefideracol）的市场。从假单胞菌发出的疾病（Cefideracol）。在假单胞菌中的发展表明，在基因组含量中，基因组含量的较小差异也可能对具有潜力的耐药性产生广泛的影响。先前的工作表明，单个“可增强性基因”可以影响假单胞菌是否可以进化对抗生素头孢嗪的高水平耐药性。但是，我们目前不知道这种机制通常运作的程度。具体而言，关于（i）对（i）耐药性如何在不同的抗生素类别中变化的知之甚少，（ii）不同的效率机制对于单毒素和多毒物耐药性是否起作用，以及（iii）是否破坏这种基因可以维持或恢复抗生素敏感性，或恢复抗生素敏感性。为了解决这些问题，我们将使用一种多学科实验的能力来解决一个差异，即对相比的综合技术，可以实现强大的技术。使细菌进化抗性。这种方法结合了高通量实验进化和细菌表型与整个基因组测序和比较基因组学。我们将在单抗生素环境和多种抗生素环境下进化来自八个假单胞菌的近60,000个独立人群。我们将将基因组含量的差异与会遇到高级抗性的每个物种获得的突变差异联系起来。然后，我们将使用现代基因组编辑技术来查看破坏可发展性基因是否可以限制抗药性，或恢复已经抵抗的生物中的敏感性。这些大规模平行的实验将揭示抗性可转化性的基因组基础，同时还揭示了高级耐药性和染色体突变之间的联系。该项目将促进我们对这些经济重要细菌中抗药性演变的增强的了解。它还将提供一个框架，我们可以从中确定遗传标记来预测抗性演化的风险，从而更好地靶向抗菌剂。最后，它将提供一个测试反透明性方法的框架，以防止抵抗力和恢复灵敏度。