Molecular mechanisms underlying the host range of bacteriophages infecting Shiga toxin-producing Escherichia coli strains

噬菌体是所有生境中最丰富的实体，也是遗传多样性的主要储存库，影响微生物结构和生态系统动态。尽管假设所有细胞生物都是病毒攻击的牺牲品，但宿主与病毒相互作用的范围却知之甚少。志贺产毒大肠埃希菌(STEC)是一类广泛存在的人畜共患病的病原体，在世界范围内引起食源性疾病。新的致病血清群不断出现，但牛及其环境仍然是STEC的主要宿主。有效的收获前干预对于最大限度地减少食品供应链中的STEC污染至关重要。内源性噬菌体普遍存在于牛及其环境中，通过未知的机制调节STEC的多样性。获得有关噬菌体如何适应牛环境和捕食各种STEC的机制见解，对于了解STEC生态和加强噬菌体生物防治结果以减少STEC在牛中的脱落至关重要。支持噬菌体-细菌相互作用的分子机制编码在噬菌体和宿主基因组中。我的研究计划的长期目标是了解环境噬菌体基因组如何变化并与细菌共同进化，以及这如何塑造细菌群落结构和种群。利用包括基因组学、生物信息学、基因组适合度分析和合成生物学在内的多种方法，我的研究项目检查了噬菌体的基因多样性和专门化，以及与STEC识别和传染性的关联。&gt；70个STEC噬菌体在3个家庭中的可用性使我们能够解决它们与宿主互动中的各种关键问题。我们将确定噬菌体尾部基因如何多样化和图案化，以响应不同的STEC表面结构。我们还将从基因上鉴定与噬菌体结合有关的STEC表面结构。对于广泛宿主范围的噬菌体，我们将探索它们是否能够识别并附着到保守的宿主表面结构以启动感染。最后，我们将使用基因组编辑来修饰噬菌体尾部基因，试图改变它们的宿主特异性。该计划首次系统地研究了不同基因型噬菌体和不同STEC血清组之间的初始相互作用，产生了关于STEC噬菌体宿主识别和感染的分子机制的新知识。解决这些研究目标将大大提高对噬菌体基因组如何适应自然环境以及这些变化如何促进新环境中的适应和专门化的理解。此外，拟议的计划旨在通过阐明初级生产水平的基本知识来应对加拿大对致病性大肠杆菌的紧迫食品安全挑战。该计划将培养出训练有素的HQP，专门从事噬菌体生物学，精通尖端技术和其他基本技能，使他们能够在学术界、工业和其他领域出类拔萃。

Bacteriophages (phages) are the most abundant entities across all habitats, and a major reservoir of genetic diversity, affecting microbial structure and ecosystem dynamics. The scope of host-viral interactions is poorly understood, although hypothetically all cellular organisms are prey to viral attack. Shiga-toxigenic Escherichia coli (STEC) are a diverse group of zoonotic pathogens, causing foodborne disease worldwide. New pathogenic serogroups keep emerging, but cattle and their environment continue to be the primary reservoir for STEC. Effective pre-harvest interventions are critical to minimize STEC contamination in the food supply chain. Endogenous phages are ubiquitous in cattle and their environment, regulating diversity of STEC via unknown mechanisms. Gaining mechanistic insights regarding how phages adapt to the cattle environment and prey on a variety of STEC is imperative to understand STEC ecology, and enhance phage biocontrol outcomes to mitigate STEC shedding in cattle. Molecular mechanisms that support phage-bacteria interactions are encoded in phage and host genomes. The long-term objectives of my research program are to understand how environmental phage genomes change and co-evolve with bacteria and how this shapes bacterial community structures and populations. Using a combination of approaches, including genomics, bioinformatics, genome-fitness assays and synthetic biology, my research program examines gene variety and specialization of phages and associated linkage to STEC recognition and infectivity. Availability of >70 STEC phages across 3 families enable us to address various key questions in their interactome with their host. We will determine how phage tail genes are diversified and patterned in response to divergent STEC surface structure. We will also genetically identify STEC surface structures involved in phage binding. For broad host-range phages, we will explore whether they can recognize and attach to conserved host surface structures to initiate infection. Finally, we will use genome editing to modify phage tail genes in an attempt to alter their host specificity. The proposed program is the first to systematically investigate initial interplays between various genotypes of phages and diverse serogroups of STEC, generating new knowledge on molecular mechanisms underlying host recognition and infection of STEC phages. Addressing these research objectives should greatly improve understanding of how phage genomes adapt in response to natural environments and how these changes promote adaptation and specialization in new environments. In addition, the proposed program aims to address Canada's urgent food safety challenges of pathogenic E. coli by elucidating fundamental knowledge at the primary-production level. This program will generate well trained HQP specialized in phage biology and proficient in cutting-edge technologies and other essential skills, enabling them to excel in academia, industry and elsewhere.