Genomics approaches to elucidating pathways to antibiotic resistance in Neisseria gonorrhoeae

项目总结/摘要 抗生素耐药性细菌的增加对公众健康构成严重威胁。在竞争中战胜易受影响的 细菌和流行率的增加，耐药菌株必须减轻耐药引起的健康成本- 赋予突变和基因。然而，并非细菌物种的每一个菌株都可以获得并维持 抗性的遗传决定因素同样好，产生了一个复杂的进化景观之间 易感性和抗性。阐明支持获取的机制的性质和多样性 和维持耐药性将使我们了解耐药菌株如何出现和传播， 从而加速开发迫切需要的新战略， 感染. 我们重点关注临床上重要的病原体淋病奈瑟菌（淋球菌），鉴于其高负担 疾病（2021年美国报告近70万例），无法治愈的感染的迫在眉睫的威胁，以及 实验操作的简易性我们的目标是定义支持获得的遗传网络， 维持耐药性的最重要的临床抗生素的N。淋病治疗：最后 批准的抗生素，头孢曲松;环丙沙星，用于定向治疗的快速诊断被批准， 欧洲;以及3期试验中的两种药物，zoliflodacin和gepotidacin。为此，我们将利用数据集 包括约18，000个临床分离株的基因组序列和抗生素敏感性谱以及一个文库 数百种临床分离株，代表了物种多样性。我们将使用计算和 实验方法，包括人口遗传学和统计工具，以确定遗传差异的亚， 群体;高通量条形码文库和实验进化，以确定影响 抗性获得作为遗传背景的函数;基因组操作以验证 基因型和抗性表型;以及阐明这些遗传位点如何影响抗性的机制研究。 易感性和抗性之间的适应度景观。 我们希望这些研究的结果将确定有助于 获得和维持耐药性的抗生素最高的临床重要性，在N。淋病 这些结果可应用于改善临床管理策略和公共卫生监测 努力此外，我们建立的系统可用于进一步探讨N.淋病 并为类似系统的开发提供了一个框架， 其他细菌病原体。

PROJECT SUMMARY/ABSTRACT The rise of antibiotic resistant bacteria poses a grave threat to public health. To outcompete susceptible bacteria and increase in prevalence, resistant strains must mitigate fitness costs incurred by resistance- conferring mutations and genes. However, not every strain of a bacterial species can acquire and maintain genetic determinants of resistance equally well, yielding a complex evolutionary landscape between susceptibility and resistance. Elucidating the nature and diversity of the mechanisms that support acquisition and maintenance of resistance will allow us to understand how resistant strains emerge and spread and thereby accelerate development of desperately needed new strategies to prevent and treat resistant infections. We focus on the clinically important pathogen Neisseria gonorrhoeae (the gonococcus), given its high burden of disease (nearly 700,000 reported cases in the US in 2021), the imminent threat of untreatable infection, and the ease of experimental manipulation. Our goal is to define the genetic networks that support acquisition and maintenance of resistance to the most clinically important antibiotics for N. gonorrhoeae treatment: the last approved antibiotic, ceftriaxone; ciprofloxacin, for which rapid diagnostics for directed therapy are approved in Europe; and the two drugs in Phase 3 trials, zoliflodacin and gepotidacin. To do so, we will leverage a dataset that includes genome sequences and antibiotic susceptibility profiles for ~18,000 clinical isolates and a library of hundreds of selected clinical isolates, representing the species diversity. We will use computational and experimental methods, including population genetics and statistical tools to identify genetic differences in sub- populations; high-throughput bar-coded library and experimental evolution to define the loci that impact resistance acquisition as a function of genetic background; genome manipulation to validate links between genotype and resistance phenotype; and mechanistic studies to elucidate how these genetic loci influence the fitness landscape between susceptibility and resistance. We expect that the results from these studies will define the stepping-stone mutations that contribute to acquisition and maintenance of resistance to the antibiotics of highest clinical importance in N. gonorrhoeae. These results can be applied to improving clinical management strategies and public health surveillance efforts. Moreover, the system we establish here can be used to further probe the biology of N. gonorrhoeae and provides a framework for the development of similar systems to dissect the genetic networks of resistance in other bacterial pathogens.