Temporal changes to cellular bioenergetics, cholesterol metabolism, innate immune responses and microbiota during infection

细菌感染是5岁以下儿童发病和死亡的主要原因，特别是在低收入和中等收入国家。在工业化国家，细菌感染主要影响老年人（社区和医院）和免疫功能低下者（例如接受化疗或感染艾滋病毒的患者）。虽然用抗生素治疗细菌感染的能力可以说是现代医学最重要的成就，但在人类医学和牲畜中广泛滥用和过度使用抗生素导致了抗菌素耐药性（AMR）的上升和传播。抗生素耐药性的威胁已得到充分报道，近年来在许多报纸文章、高级别政府报告和运动中都看到了这一点。抗生素耐药细菌已经造成每年70万人死亡，预计到2050年将造成惊人的1000万人死亡。虽然耐多药细菌的传播急剧增加，但在过去几十年里，新抗生素的发现率大幅下降，只有少数新批准的药物进入临床。这突出了迫切需要用治疗细菌感染的新方法来补充传统的药物发现途径。重要的是，抗生素的意外目标包括正常的、有益的肠道细菌（微生物群）。因此，我们需要采用创新的方法来治疗细菌感染，从而最大限度地减少选择性压力促进耐药性的出现和对微生物群的影响。有效和新型控制措施的发展需要对疾病的生物学有系统的了解，特别是在肠道微生物群的背景下，细菌病原体与其宿主之间复杂的相互作用。根据定义，这种类型的研究依赖于利用强大的和生理学相关的动物模型。啮齿柠檬酸杆菌是小鼠特有的细胞外病原体，它与人类致病性大肠杆菌菌株（如大肠杆菌O157）具有相同的感染策略。作为一种天然的小鼠病原体，啮齿鼠为研究肠道病原体在自然宿主和肠道微生物群中的感染提供了理想的模型。啮齿c引起自限性感染，并引发强大的免疫反应，上皮细胞增殖和正常肠道细菌的移位，这些细菌模仿人类感染致病性大肠杆菌时观察到的特征。最近，通过应用最先进的分子方法来研究啮齿鼠与肠道细胞的相互作用，我们发现感染会导致宿主细胞的能量产生和中枢代谢发生剧烈变化，这似乎是一种抑制炎症的尝试。虽然以前的重点一直放在免疫细胞上，但直到现在我们才开始意识到控制上皮细胞的代谢是宿主-病原体相互作用的另一个关键前沿。在这个项目中，我们的目标是在整个生物体的背景下，在感染期间获得宿主-病原体相互作用的前所未有的分子分辨率。我们的概念验证研究已经表明，在C.啮齿动物感染期间，胆固醇的产生和释放被解除管制。在这个项目中，我们将使用野生型和突变型啮齿鼠菌株，以及野生型小鼠和缺乏胆固醇代谢关键控制因子的小鼠。我们将研究代谢随时间的变化，从感染到恢复，并将这些变化与特定肠道微生物群的存在相匹配。使用选定的突变体，包括细菌和宿主，将使我们能够解开所涉及的分子过程。我们相信我们的开创性方法将导致对宿主细菌感染的理解的概念转变，从而为开发新的细菌感染治疗策略开辟新的途径。

Bacterial infections are major cause of morbidity and mortality in children under 5 years of age, especially in Low and Middle Income Countries (LMIC). In industrial countries, bacterial infections mainly affect the elderly (both in the community and in hospitals) and the immunocompromised (e.g. patients undergoing chemotherapy or infected with HIV). While the ability to treat bacterial infections with antibiotics is arguably the most important achievement of modern medicine, the extensive misuse and overuse of antibiotics in human medicine and livestock has contributed to the rise and spread of antimicrobial resistance (AMR). The threat of antibiotic resistance is well reported, being sighted in many newspaper articles, high-level government reports and campaigns in recent years. Already responsible for 700,000 deaths per year, antibiotic-resistant bacteria are predicted to cause a staggering 10 million deaths by 2050. Whilst there has been a dramatic rise in the spread of multi-drug resistant bacteria, the discovery rate of new antibiotics has tumbled over the past decades, with only a few new approved drugs reaching the clinic. This highlights the urgent need to complement traditional drug discovery routes with new approaches to treat bacterial infections. Importantly, unintended targets of antibiotics include the normal, beneficial, gut bacteria (microbiota). Accordingly, we need to employ innovative approaches to treat bacterial infections, which minimise both selective pressure-promoting emergence of resistance and impact on the microbiota. The development of effective and novel control measures requires a systematic understanding of the biology of the disease, particularly the complex interactions between bacterial pathogens and their hosts in the context of the gut microbiota. By definition, this type of research relies on utilisation of robust and physiologically relevant animal models.Citrobacter rodentium is mouse specific extracellular pathogen, which shares an infection strategy with human pathogenic E. coli strains (for example E. coli O157). Being a natural mouse pathogen, C. rodentium provides an ideal model to study infections with gut pathogens in the natural host and in the context of the gut microbiota. C. rodentium causes a self-limiting infection and triggers robust immune responses, proliferation of epithelial cells and displacement of the normal gut bacteria which mimic the characteristics observed during human infection with pathogenic E. coli. Recently, by applying state-of-the-art molecular methods to study the interaction of C. rodentium with cells that line the gut we found that the infection causes drastic changes to energy production and central metabolism in the host cells, in what seems to be an attempt to dampen inflammation. While previously the focus has been on immune cells, it is only now that we are starting to realise that controlling metabolism in epithelial cells is another key frontier in host-pathogen interactions. In this project we aim to obtain an unprecedented molecular resolution of host-pathogen interactions over the duration of infection, in the context of a whole organism. Our proof-of-concept studies have already shown deregulation in the production and release of cholesterol during C. rodentium infection. In this project we will use wild type and mutant C. rodentium strains as well as wild type mice and mice deficient in a key controllers of cholesterol metabolism. We will study changes in metabolism over time, from infection to recovery, and match these changes to the presence of specific gut microbiota. The use of selected mutants, both bacterial and host, will allow us to unravel the molecular processes involved. We believe our pioneering approach would lead to conceptual shifts in understanding of host-bacterial infections and thus open new avenues for the development of novel treatment strategies for bacterial infection.