Soil survival and re-emergence, the continued threat of plague

假设、理论基础和意义。鼠疫耶尔森菌是鼠疫的病原，是人类最具破坏性的传染病之一，在人类历史上占有重要地位。跳蚤和老鼠与该疾病的传播有关，早在1914年就有研究表明，这种传播模式已成为科学教条。普遍接受的观点是，在根深蒂固的啮齿动物种群中，地方性鼠疫事件确保鼠疫杆菌通过跳蚤在部分耐药宿主种群中传播，并在传播到动物宿主后迅速传播。因此，鼠疫杆菌在人群中重新出现之前在相关宿主中传播。尽管这种优雅的传播模式一直存在，但它过于简化了。例如，在没有人间病例或大规模啮齿动物死亡的地方，鼠疫往往在爆发几十年后重新出现，例如分别在阿尔及利亚、利比亚、马达加斯加和印度暴发57年、25年、60年和30年后。考虑到鼠疫杆菌是由一种几乎相同的(大约。98% DNA同一性)自由生活土壤传播的胃肠道病原体祖先，假结核耶尔森菌，表面上随机的鼠疫死灰复现事件很可能实际上是由于细菌在高度多样化的生态条件下通过在土壤中采取“坐等”的生活方式而存活。然而，用于实验室鼠疫杆菌生存实验的土壤样本几乎总是经过消毒的，此类实验通常假设鼠疫杆菌可以独立生存，而忽略了生存策略，如土壤中生物膜的形成或与其他细菌、真菌、原生动物或线虫的结合。已知鼠疫耶尔森菌对滋养体的捕食具有抗性，并能在盘状盘齿柱和castellanacanthamoeba中存活并在细胞内复制，而且鼠疫耶尔森菌和假结核耶尔森菌也能定植于土壤中的线虫秀丽隐杆线虫。目的：控制土壤鼠疫菌生活方式的生物学和分子机制的基本生物学问题尚未得到调查，作为世界卫生组织分类的重新出现的病原体，在世界一些地区仍然流行，我们对鼠疫生物学的认识存在重大差距，这令人严重关切。因此，本博士项目旨在通过解决以下研究问题，深入研究土壤环境以及相关的变形虫和线虫如何在动物流行期间成为鼠疫杆菌的重要宿主。1. 土壤环境如何影响鼠疫杆菌的生存？2. 线虫和变形虫的存在是否会提高土壤中鼠疫杆菌的存活率？3. 鼠疫杆菌在土壤中生存的关键基因和分子机制是什么？这些问题将通过多种方法来解决，包括土壤生物膜持久性测定、变形虫和线虫感染测定以及基因组学和转录组学研究、转座子插入测序技术和靶向基因突变。该项目将适合对分子遗传学和传染病有浓厚兴趣的学生，并乐于接受在3级隔离条件下工作的培训。最近NERC的大量资助将持续到2026年，这意味着该学生将融入一个团队，从事该项目的互补方面的工作，因此将得到全程支持。

Hypothesis, Rationale and Significance.As the causative agent of plague, Yersinia pestis occupies a prominent place in human history as one of the most destructive infectious human diseases. Fleas and rats have been associated with the spread of the disease with research dating back as far as 1914 ensuring that this model of transmission has become scientific dogma. The general acceptance being that within an inveterate rodent population, enzootic plague episodes ensure Y. pestis is passed through a partially resistant host population by fleas and upon transmission into epizootic hosts plague rapidly spreads. Y. pestis is therefore circulating in associated hosts prior to re-emergence in the human population. Although the elegance of this model of transmission has endured, it is hugely oversimplified. For example, in locations where there have been no human cases or mass rodent die-offs, plague often re-emerges decades after an outbreak such as in Algeria, Libya, Madagascar and India 57, 25, 60 and 30 years later respectively. Given that Y. pestis evolved from a near identical (approx. 98% DNA identity) free-living soil borne gastrointestinal pathogen ancestor, Yersinia pseudotuberculosis, it is highly likely that apparently random plague resurgence events are actually due to the bacteria surviving under highly diverse ecological conditions by adopting a 'sit and wait' lifestyle in soil. However, soil samples used for laboratory Y. pestis survival experiments are almost always sterilized and such experiments generally assume that Y. pestis would survive independently and overlook survival strategies such as biofilm formation in soils or in association with other bacteria, fungi, protozoa or nematodes. It is already known that Y. pestis is resistant to trophozoite predation and can survive and replicate intracellularly in Dictyostelium discoideum and Acanthamoeba castellani and both Y. pestis and Y. pseudotuberculosis can also colonise the soil-dwelling nematode worm Caenorhabditis elegans, which has been exploited as an infection model for biotic surface biofilm formation.Objectives.Fundamental biological questions underlying the biology and molecular mechanisms controlling the soil-dwelling Y. pestis lifestyle have not been investigated and as a WHO classified re-emerging pathogen which is still endemic in some parts of the world, this significant gap in our understanding of plague biology is of grave concern.This PhD project therefore aims to conduct an in-depth study to understand how the soil environment, and associated amoebae and nematodes act as significant reservoirs for Y. pestis during inter-epizootic episodes by addressing the following research questions. 1. How do soil environments impact on Y. pestis survival? 2. Does the presence of nematodes and amoeba enhance Y. pestis survival in soil? 3. What are the key genes and molecular mechanisms involved in Y. pestis survival in soil? These questions will be addressed using a variety of approaches including biofilm persistence assays in soils, amoebae and nematodes infection assays along with genomic and transcriptomic studies, transposon insertion sequencing technologies and targeted gene mutations. The project will be suitable for a student who has a keen interest in molecular genetics and infectious disease and is happy to train to work under containment level 3 conditions. Recent substantial NERC funding through to 2026 means that the student will embed into a team working on complementary aspects of this project and will therefore be fully supported throughout.