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

假设、理论基础和意义作为鼠疫的病原体，鼠疫耶尔森氏菌作为最具破坏性的人类传染病之一，在人类历史上占有突出的地位。跳蚤和老鼠一直与疾病的传播有关，早在1914年的研究就确保了这种传播模式已经成为科学教条。人们普遍认为，在根深蒂固的啮齿动物种群中，地方性鼠疫发作确保鼠疫杆菌通过跳蚤通过部分抗药性宿主种群传播，并在传播到流行病宿主后迅速传播。因此，鼠疫耶尔森氏菌在人类重新出现之前在相关宿主中传播。尽管这种传输模式的优雅延续了下来，但它过于简单化了。例如，在没有人类病例或大规模啮齿动物死亡的地方，鼠疫往往在疫情爆发几十年后重新出现，例如分别在57年、25年、60年和30年后在阿尔及利亚、利比亚、马达加斯加和印度。鉴于鼠疫耶尔森氏菌是从一个几乎相同的(约.98%的DNA同一性)自由生活的土壤传播的胃肠道病原体祖先假结核耶尔森菌，很可能表面上随机的鼠疫死灰复燃事件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“静坐等待”的生活方式而生存下来的。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灭菌的，这类实验通常假设鼠疫杆菌将独立生存，而忽略了生存策略，如在土壤中形成生物膜或与其他细菌、真菌、原生动物或线虫结合。众所周知，鼠疫杆菌对滋养体的捕食具有抵抗力，可以在盘状念珠菌和卡氏棘阿米巴中存活并在细胞内复制，鼠疫杆菌和假结核杆菌也可以在土壤寄生的线虫上定植，作为生物表面生物膜形成的感染模型。目的控制土壤寄生的鼠疫杆菌生活方式的生物学和分子机制的基本生物学问题尚未被研究，并被世界卫生组织归类为新出现的病原体，在世界一些地区仍然流行。因此，这一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阿米巴和线虫如何在鼠疫流行间期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存活？2.线虫和阿米巴的存在是否提高了鼠疫杆菌在土壤中的存活？3.鼠疫杆菌在土壤中存活的关键基因和分子机制是什么？这些问题将通过各种方法解决，包括土壤中生物膜持久性分析、阿米巴和线虫感染分析以及基因组和转录组研究、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级遏制条件下工作的培训。到2026年，NERC最近提供了大量资金，这意味着学生将被嵌入到一个团队中，致力于这个项目的补充方面，因此将在整个过程中得到全力支持。

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.