A pipeline technology for discovery of new antibiotics from Streptomyces

现代医学不可避免地面临着“超级细菌”形式的严峻挑战-对一线抗生素具有耐药性的致病细菌。医学中的抗生素时代已经跨越了过去70年，第一批药物青霉素和链霉素于20世纪40年代末推出。与细菌感染相关的死亡率急剧下降，许多新抗生素的发现也是如此，在20世纪80年代达到顶峰。从那时起，新抗生素的发现急剧下降，一线抗生素耐药性的发生率和这些耐药细菌感染导致的患者死亡率都有所增加。大多数抗生素是由土壤细菌产生的，称为链霉菌。最近对这些细菌的代表性物种进行的基因组测序项目显示，它们具有许多“神秘的”抗生素生物合成途径;也就是说，它们具有产生比以前意识到的更多抗生素的遗传潜力。由戴森协调的欧洲合作研究项目ActinoGEN的结果表明，这些神秘的途径不是遗传遗迹，但可以被激活以指导新抗生素的生产。因此，我们现在可以将过去70年解释为发现“唾手可得的果实”（我们当前的一线抗生素）的初始时期。此后，发现的成功率下降了。目前的挑战是收获大量的高挂果实，即神秘途径的产物，并扩大可用于医学的抗生素的范围。目前，这样做的方法非常耗时，依赖于首先获得和分析链霉菌属物种的基因组序列，然后进行基因工程以激活隐藏的途径。该提案通过设计一种廉价的菌株操作方法，再加上对广泛的链霉菌菌株文库进行高通量筛选，以发现隐藏途径的新抗生素产物，从而解决了技术差距。菌株操作涉及快速和协同的方法来激活和过度生产新的抗生素。为了证明原理，获得了过量生产新型抗生素的操纵菌株，然后我们将分析抗生素并确定指导其合成的隐蔽生物合成途径。该技术的成功演示将随后导致其被采用，以发现与制药/生物技术部门的工业合作伙伴合作在大型菌株库中生产的新抗生素。

It is inescapable that modern medicine is faced with a severe challenge in the form of 'Superbugs' - disease-causing bacteria that are resistant to front-line antibiotics. The antibiotic era in medicine has spanned the last 70 years with the first drugs, penicillin and streptomycin, being introduced in the late 1940's. A dramatic reduction in fatalities associated with bacterial infections followed, as did the discovery of many new antibiotics, reaching a peak in the 1980's. Since then, there has been a dramatic decline in new antibiotic discovery, and an increase both in the incidence of resistance to front-line antibiotics and in patient fatalities due to infections by these resistant bacteria. The majority of antibiotics are produced by soil bacteria called Streptomyces. Recent genome sequencing projects with representative species of these bacteria have revealed that they possess many 'cryptic' antibiotic biosynthetic pathways; that is they have the genetic potential to produce many more antibiotics than previously realised. An outcome of a European collaborative research project, ActinoGEN, coordinated by Dyson, indicates that these cryptic pathways are not genetic relics but can be activated to direct production of new antibiotics. Consequently we can now interpret the last 70 years as an initial period during which 'low-hanging fruit', our current front-line antibiotics, were discovered. Thereafter, the success in discovery has declined. A current challenge is now to harvest the plentiful higher-hanging fruit, the products of the cryptic pathways, and extend the range of antibiotics that can be used in medicine. The ways to do this are at present very time-consuming, dependent on first obtaining and analysing the genome sequences of Streptomyces species, before genetic engineering to activate a cryptic pathway. This proposal addresses a technological gap by devising a means of inexpensive strain manipulation coupled with high-throughput screening of extensive Streptomyces strain libraries to discover new antibiotic products of cryptic pathways. The strain manipulations involve rapid and synergistic approaches to activate and over-produce new antibiotics. To demonstrate a proof-of-principle, having obtained manipulated strains over-producing a novel antibiotic, we will then analyse the antibiotic and determine the cryptic biosynthetic pathway that directs its synthesis. Successful demonstration of the technology will subsequently lead to its adoption to discover new antibiotics produced in large strain collections, in collaboration with industrial partners from the pharmaceutical/biotech sector.