Understanding mechanisms of synergy between bacterial anti-phage defences. (4566)

抗生素耐药性（AMR）是当今人类健康面临的最大威胁之一。移动的遗传元件（MGE），如DNA和质粒，在AMR传播中起着关键作用，但也为开发替代抗菌药物提供了一种有前途的工具。MGE的传播从根本上由细菌防御系统决定，细菌防御系统可以阻断AMR并限制基于噬菌体的治疗的疗效。这种防御的很好例子是限制性修饰（RM）和CRISPR-Cas系统，这两种系统都彻底改变了我们的DNA操纵能力。至关重要的是，近年来发现了数量惊人的其他防御措施。但是，这些防御机制在阻断MGE感染方面有多重要？它们总是单独起作用还是与其他防御机制协同作用？这个问题在货车Houte教授（埃克塞特大学）和Szczelkun教授（布里斯托大学）的一个跨学科项目中得到了解决，与来自利物浦，巴斯，达勒姆，圣安德鲁斯和埃克塞特的团队合作，他们都是最近资助的BBSRC sLoLa网络的一部分，你将自动成为其中的一部分。您将使用一组300个人类病原体铜绿假单胞菌的测序分离株来研究防御系统之间的协同作用以及这如何影响MGE感染性。初步分析表明，这些菌株平均每个基因组有8个不同的防御系统，菌株之间存在巨大差异（最小2，最大2）。您将使用各种生物信息学方法来了解这些分离株的基因组中优先共存的防御。然后，您将使用一组不同的细菌对分离物进行大规模感染检测，以建立噬菌体感染性/抗性和防御组合之间的相关性。将防御组合的基因组工程改造成参考菌株将用于确定这些观察到的相关性是否具有因果关系。为了确定微生物是否以及如何进化以克服防御组合，您将使用基于NanoPore测序的新型测序方法。最后，您将使用单细胞显微镜在单个细胞水平上研究防御组合的后果。您将主要在埃克塞特康沃尔校区的Stineke货车Houte教授的实验室工作，他是Lister奖研究员和ERC资助保持器持有者，拥有一支蓬勃发展和不断扩大的团队，致力于AMR，CRISPR-Cas抗菌工具开发和MGE-细菌相互作用。在整个项目中，您将与布里斯托的Szczelkun教授实验室以及sLoLa网络的其他成员密切合作。

Antimicrobial resistance (AMR) poses one of the greatest threats to human health of our time. Mobile genetic elements (MGEs), such as phages and plasmids, play a key role in AMR dissemination, but also present a promising tool for development of alternative antimicrobials. The spread of MGEs is fundamentally shaped by bacterial defence systems, which can block AMR and limit the efficacy of phage-based therapies. Good examples of such defences are Restriction-Modification (RM) and CRISPR-Cas systems, both of which have revolutionised our DNA manipulating abilities. Crucially, an astonishing number of other defences have been discovered in recent years. But how important are these defences in blocking MGE infection, and do they always work on their own or in concert with other defences?This question is addressed in an interdisciplinary project in the groups of Prof van Houte (Univ of Exeter) and Prof Szczelkun (Univ of Bristol), with collaborations with teams from Liverpool, Bath, Durham, St Andrews and Exeter, who are all part of a recently funded BBSRC sLoLa network that you will automatically become part of. You will use a set of 300 sequenced isolates of the human pathogen Pseudomonas aeruginosa to investigate synergy between defence systems and how this impacts MGE infectivity. Preliminary analysis show that these isolates have on average 8 different defence systems/genome, with huge variation between isolates (min. 2, max. 18 systems/genome).You will use various bioinformatics approaches to understand which defences preferentially co-occur in genomes of these isolates. You will then carry out large-scale infection assays on the isolate collection using a panel of different phages to establish correlations between phage infectivity/resistance and defence combinations. Genome engineering of defence combinations into a reference strain will be used to determine whether these observed correlations have a causal relationship. To establish if and how phages can evolve to overcome defence combinations, you will use novel sequencing methodologies based on NanoPore sequencing. Finally, you will study the consequences of defence combinations at the individual cell level using single cell microscopy.You will be primarily based in the lab of Prof Stineke van Houte at Exeter's Cornwall campus, who is a Lister prize fellow and ERC grant holder with a thriving and expanding team working on AMR, CRISPR-Cas antimicrobial tool development, and MGE-bacteria interactions. Throughout the project you will work in close collaboration with Prof Szczelkun's lab in Bristol, and other members of the sLoLa network.