Epidemiological investigation of emerging infectious diseases of farmed fish in Canada

对海产品需求的增加导致水产养殖业的快速增长，包括以网笼为基础的鲑鱼生产。加拿大的2040年蓝色经济战略设想加拿大成为三大最佳可持续海产品生产国。然而，该行业面临着海洋生态系统中传染病出现、严重程度和流行程度增加的挑战。许多水生动物疾病与微生物群落结构的显著变化或水库无毒祖先变异的遗传和功能变化有关。Mouthrot（MR;传染性鲑鱼贫血症（ISA）和传染性鲑鱼贫血症（伊萨）是加拿大大西洋鲑鱼水产养殖中出现的疾病，是威胁鲑鱼水产养殖可持续性的最重要的细菌性和病毒性疾病。海洋韧杆菌是二尖瓣返流的主要病原体;然而，其他韧杆菌属也可能参与。伊萨病毒的无毒毒株很可能是农场环境中存在的宿主，从中出现毒毒株。然而，加拿大水产养殖业的流行病学和与疾病爆发和严重程度相关的因素大多是未知的。我们推测，这些疾病中涉及的传染性病原体作为机会性病原体存在于农场中，并且其暴发涉及多因素病因学。我们还假设，爆发是由于压力因素（如水温升高、管理等）导致受影响鱼类的病原体和/或微生物群落结构的遗传组成发生变化所致。我在农场进行观察研究的短期目标是阐明宿主、病原体和环境之间的相互作用，以了解疾病的发生、传播、和风险因素与这些新出现的传染病在加拿大鲑鱼水产养殖使用MR和伊萨的例子。我的研究计划的长期目标是了解不断变化的生态系统的影响，以及农场和野生动物的相互作用，以加强可持续水产养殖和渔业的水生流行病学研究计划。这项研究将回答的一些问题是：传染性病原体的非毒性菌株有多丰富，它们转化为毒性菌株并导致临床爆发的可能性有多大？环境和其他因素在多大程度上与这些微生物和遗传变化相互作用？关于传染性病原体的基因组特征和确定疾病出现所涉及的因素的关键结果将有助于通过制定短期缓解策略和减少抗生素使用来有效管理疾病，为预防疫情提供知情指导，并有助于实现加拿大蓝色经济战略2040年长期可持续海洋食品生产目标。关于养殖鱼类中这些疾病的流行病学知识有可能用于减轻其对野生鲑鱼的影响。

The increase in demand for seafood has led to rapid growth of aquaculture industry, including netpen based salmon production. Canada's Blue Economy Strategy 2040 envisions Canada to be top three best sustainable producer of seafood. However, the industry is challenged by an increase in the emergence, severity, and prevalence of infectious diseases in the marine ecosystem. Many aquatic animal diseases are associated with pronounced shifts in microbial community structures or genetic and functional changes in reservoir non-virulent progenitor variants. Mouthrot (MR; tenacibaculosis), and infectious salmon anemia (ISA) are emerging diseases in Atlantic salmon aquaculture in Canada, the most important bacterial and viral diseases threatening the sustainability of salmon aquaculture. Tenacibaculum maritimum is the principal causative agent of MR; however, other Tenacibaculum spp are also likely involved. The non-virulent strains of the ISA virus are likely the reservoir present in the farm environment, from which the virulent strains emerge. However, the epidemiology and factors associated with outbreaks and severity of disease are mostly unknown for Canadian aquaculture. We surmise that infectious agents involved in these diseases are present on the farms as opportunistic agents and that a multifactorial etiology is involved in their outbreaks. We also hypothesize that outbreaks result from changes in the genetic make-up of the agent and, or microbial community structure in the affected fish due to stressors, such as increased water temperature, management, etc. The short-term goal of my on-farm observational research is to elucidate the interactions between host, pathogen(s), and environment to understand the occurrence, transmission, and risk factors associated with these emerging infectious diseases in salmon aquaculture in Canada using MR and ISA as example cases. The long-term goal of my research program is to understand the effects of changing ecosystems, and farm and wild interactions to enhance the aquatic epidemiology research program for sustainable aquaculture and fishery. Some of the questions this research will answer are: how abundant are non-virulent strains of infectious agents, and how likely are they to convert to virulent strains and result in clinical outbreaks? To what extent do the environmental and other factors interact with these microbial and genetic shifts? Key results on the genomic characteristics of the infectious agents and the identification of factors involved in the emergence of disease will help in efficient management of the disease by formulating mitigation strategies in the short term and reducing antibiotic use, providing informed guidance for outbreak prevention and help achieve Canada's Blue Economy Strategy 2040 sustainable sea food production target in the long term. Knowledge gained on the epidemiology of these diseases in farmed fish can potentially be applied to mitigate their impact on wild salmon.