Untangling gene regulatory networks controlling host-pathogen interactions of the antimicrobial-resistant human pathogen Klebsiella pneumoniae

在过去的几十年里，由于多重耐药细菌病原体引起的感染有所增加，抗生素耐药细菌的出现是我们这个时代的主要挑战之一。这种对人类健康的严重威胁导致了令人担忧的治疗选择的局限性，特别是针对所谓的ESKAPE病原体（屎肠球菌、金黄色葡萄球菌、克雷伯氏菌）。肺炎克雷伯氏菌是医院和社区获得性感染的重要原因，在老年人和免疫功能低下者中引起例如肺炎、皮肤/伤口感染和导管相关性尿路感染。K.的处理肺炎克雷伯氏菌感染受到多重耐药和高毒力菌株的全球传播的阻碍，并且碳青霉烯类耐药的克雷伯氏菌。肺炎被WHO列为新药开发的关键优先事项。特别值得关注的是全球传播的ST 258菌株的碳青霉烯类耐药分离株，这种菌株经常引起医院相关的爆发，并且是碳青霉烯类耐药基因传播的主要原因，因为它们在一段移动的DNA上携带这些基因，这些基因很容易传播给其他细菌。临床分离的克雷伯氏菌。肺炎克雷伯氏菌可被分类为经典菌株或高毒力菌株;虽然高毒力菌株是严重的公共卫生威胁，但目前大多数克雷伯氏菌属疾病负担与经典菌株相关。K.肺炎克雷伯氏菌利用许多不同的毒力因子保护自己免受宿主免疫反应的影响，这些毒力因子包括保护性胶囊、其他表面结构和蛋白质，这些蛋白质使肺炎克雷伯氏菌粘附在宿主细胞上。这些毒力因子中最重要的毒力因子目前仅限于高毒力菌株，并且在大多数经典克雷伯氏菌中缺失。虽然我们对肺炎克雷伯氏菌的基因组了解很多，pneumoniae，我们对K.肺炎引起的疾病仍然有限。这是由于有限的感染模型，在人类之外，以及临床上重要的谱系高度多样化的事实。为了更好地管理和治疗K.因此，迫切需要对其在人类中引起疾病的能力有更深入的了解。其他人最近也展示了鼠伤寒沙门氏菌（克雷伯氏菌的亲戚）是如何通过“隐藏”在被称为巨噬细胞的宿主免疫细胞内来逃避抗生素的杀伤的，但是K。大多数人认为肺炎克雷伯氏菌缺乏这种能力。然而，我们最近发现，出乎意料的是，一个K。pneumoniae ST 258菌株可以在巨噬细胞内积极复制，我们计划尝试了解这一过程，以便为更好地治疗K.在这个项目中，我们将研究这种菌株如何通过改变其调节代谢和生长的方式来应对巨噬细胞内的生存，以及宿主细胞如何应对入侵细菌。我们将尝试重建细菌中调节这种能力的复杂控制网络，并将这种反应与其他在巨噬细胞内存活的相关细菌的反应进行比较。最后，我们将研究K.从环境中，社区中的人们和医院的病人中分离出肺炎，看看这种能力在宿主细胞中的生存范围有多广，看看我们是否能识别出任何可能解释这一点的基因或基因变异。我们相信，了解所有这些方面将加快努力，以产生治疗K。肺炎感染。

The last decades have seen a rise in infections due to multi-drug-resistant bacterial pathogens, and the emergence of antibiotic resistant bacteria is one of the major challenges of our time. This serious threat to human health leads to worrying limitations of treatment options, especially against the so-called ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, K. pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) and we risk an "apocalyptic" post-antibiotic era if urgent action is not taken.The bacterium Klebsiella pneumoniae is an important cause of hospital- and community-acquired infections, causing for example pneumonia, skin/wound infections and catheter-associated urinary tract infections in the elderly and immunocompromised. Treatment of K. pneumoniae infections is hindered by the global spread of multidrug-resistant and hypervirulent strains, and carbapenem-resistant K. pneumoniae are classified by the WHO as a critical priority for new drug development. Of special concern are carbapenem-resistant isolates of the globally spreading strain called ST258 which frequently cause hospital-associated outbreaks and are a major contributor to the spread of carbapenem-resistance genes as they carry these on a piece of mobile DNA that can be easily spread to other bacteria. Clinical isolates of K. pneumoniae can be classified as classical or hypervirulent strains; while hypervirulent strains are a serious public health threat, the majority of Klebsiella disease burden is currently associated with classical strains. K. pneumoniae protects itself from the host immune response using many different virulence factors including a protective capsule, other surface structures and proteins that let it scavenge iron and stick to host cells. The most important of these virulence factors are currently limited to hypervirulent strains, and absent from the majority of classical K. pneumoniae isolates.Although we know a lot about the genomes of K. pneumoniae, our understanding of the mechanisms by which K. pneumoniae causes disease is still limited. This is due to limited models of infection, outside the human, and the fact that clinically important lineages are highly diverse. In order to better manage and treat K. pneumoniae infections, a deeper understanding of its ability to cause disease in humans is urgently needed. Others have recently shown how Salmonella Typhimurium (a relative of Klebsiella) is able to evade killing by antibiotics by "hiding" inside host immune cells called macrophages, but K. pneumoniae was largely believed to lack this ability. However, we have recently shown that unexpectedly a K. pneumoniae ST258 strain can actively replicate inside macrophages, and we plan to try to understand this process in order to provide the basis for better treatments of K. pneumoniae in the future.In this project, we will investigate how this strain responds to surviving inside macrophages by changing how it regulates its metabolism and growth, and how the host cell responds to the invading bacteria. We will try to reconstruct the complex control networks that regulates this ability in the bacterium, and we will compare this response to that of other related bacteria that also survive inside macrophages. Finally, we will look at other strains of K. pneumoniae from the environment, people in the community and hospital patients to see how widespread the ability is to survive inside host cells, and see if we can identify any genes or gene variants that might explain this. We believe that understanding all of these aspects will accelerate efforts to produce treatments for K. pneumoniae infection.