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

抗菌素耐药性(AMR)是当今人类健康面临的最大威胁之一。移动遗传元件(MGES)，如噬菌体和质粒，在AMR的传播中起着关键作用，但也为开发替代抗微生物药物提供了一个很有前途的工具。MGES的传播从根本上是由细菌防御系统造成的，该系统可以阻止AMR并限制基于噬菌体的疗法的疗效。这种防御的很好的例子是限制修饰(RM)和CRISPR-CAS系统，这两个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。但这些防御措施在阻止MGE感染方面有多重要？它们总是单独发挥作用，还是总是与其他防御措施协同工作？范胡特教授(埃克塞特大学)和什切尔昆教授(布里斯托尔大学)的一个跨学科项目解决了这个问题，他们与来自利物浦、巴斯、达勒姆、圣安德鲁斯和埃克塞特的团队合作，这些团队都是最近资助的BSRC sLoLa网络的一部分，你将自动成为该网络的一部分。您将使用一组300个测序的人类病原体铜绿假单胞菌分离物来研究防御系统之间的协同作用以及这如何影响MGE的传染性。初步分析表明，这些分离物平均有8个不同的防御系统/基因组，分离物之间存在巨大的差异(Min.2，最大18个系统/基因组)。你将使用各种生物信息学方法来了解哪些防御系统优先出现在这些分离物的基因组中。然后，您将使用一组不同的噬菌体对分离物集合进行大规模感染测试，以建立噬菌体感染性/抵抗力与防御组合之间的相关性。将防御组合的基因组工程转化为参考菌株将被用来确定这些观察到的相关性是否具有因果关系。为了确定噬菌体是否以及如何进化以克服防御组合，你将使用基于纳米孔测序的新测序方法。最后，你将使用单细胞显微镜研究防御组合在单个细胞水平上的后果。你将主要在埃克塞特大学康沃尔校区的斯坦克·范·胡特教授的实验室工作，他是利斯特奖获得者和ERC赠款获得者，团队蓬勃发展，不断扩大，致力于AMR、CRISPR-CAS抗菌工具开发以及MGE与细菌的相互作用。在整个项目中，您将与Szczelkun教授在布里斯托尔的实验室以及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.