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

在过去的几十年里，由于耐多药细菌病原体而导致的感染增加，而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治疗选择的令人担忧的局限性，特别是对所谓的ESKAPE病原体(粪肠球菌、金黄色葡萄球菌、肺炎克雷伯菌、鲍曼不动杆菌、铜绿假单胞菌和肠杆菌)的治疗限制，如果不采取紧急行动，我们就有可能进入后抗生素时代。肺炎克雷伯菌是医院和社区获得性感染的重要原因，导致老年人肺炎、皮肤/伤口感染和导管相关尿路感染和免疫功能受损。多重耐药和超强毒力菌株的全球传播阻碍了肺炎克雷伯菌感染的治疗，耐碳青霉烯类肺炎克雷伯菌被世界卫生组织列为新药开发的关键优先事项。特别令人担忧的是全球传播的ST258菌株的碳青霉烯耐药菌株，它们经常导致医院相关疫情，是碳青霉烯耐药基因传播的主要贡献者，因为它们携带在一段可移动的DNA上，很容易传播给其他细菌。肺炎克雷伯菌临床分离株可分为经典株和超强毒株，虽然超强毒株严重威胁公共卫生，但目前克雷伯氏菌的大部分疾病负担与经典株有关。肺炎克雷伯菌使用许多不同的毒力因子来保护自己免受宿主免疫反应的影响，这些因子包括保护性衣壳、其他表面结构和蛋白质，使其能够清除铁并附着在宿主细胞上。其中最重要的毒力因子目前仅限于超强毒力菌株，而大多数经典肺炎克雷伯菌分离株都缺乏这些毒力因子。尽管我们对肺炎克雷伯菌的基因组了解很多，但我们对肺炎克雷伯菌致病机制的了解仍然有限。这是由于人类以外的有限的感染模式，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肺炎克雷伯菌感染，迫切需要更深入地了解它在人类中致病的能力。其他研究人员最近展示了鼠伤寒沙门氏菌(克雷伯氏菌的近亲)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戮，但肺炎克雷伯菌基本上被认为缺乏这种能力。然而，我们最近发现一株出人意料的肺炎克雷伯菌ST258菌株可以在巨噬细胞内活跃地复制，我们计划试图了解这一过程，以便为未来更好地治疗肺炎克雷伯菌提供基础。在本项目中，我们将研究该菌株如何通过改变其调节其新陈代谢和生长的方式来应对巨噬细胞内的生存，以及宿主细胞如何对入侵的细菌做出反应。我们将尝试重建调节细菌这种能力的复杂控制网络，并将这种反应与其他相关细菌的反应进行比较，这些细菌也存活在巨噬细胞内。最后，我们将观察来自环境、社区居民和医院患者的其他肺炎克雷伯菌菌株，看看这种在宿主细胞内生存的能力有多普遍，并看看我们是否能识别出任何可能解释这一现象的基因或基因变体。我们相信，了解所有这些方面将加快肺炎克雷伯菌感染治疗的努力。

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.