Unravelling Enterococcus cecorum infection on UK broiler farms: correlating clinical signs with genomics, persistence and animal behaviour.

致残等地方性疾病可能导致肉鸡瘫痪和死亡，这给肉鸡带来了相当大的福利问题，它导致大量使用抗菌剂，并给英国和全世界的肉鸡业造成重大经济损失。盲肠球菌，一种新兴的病原体，已经成为在英国肉鸡行业受影响的家禽群的感染。然而，由于大肠杆菌基因组学还处于起步阶段，人们对这种共生菌是如何进化成病原体的知之甚少。它所占据的导致禽群中出现明显散发疾病的环境宿主也是未知的，并且没有对动物行为进行密切监测，以确定在疾病进展和与跛行相关的总体身体变化变得明显之前，在感染的早期阶段是否发生任何细微变化。因此，在这一变革性的概念验证提案中，我们的目标是通过汇集来自不同背景的独特和高技能的项目团队来填补目前的知识空白，这些团队是通过BBSRC地方性牲畜疾病倡议启动伙伴关系研讨会聚集起来的。通过我们的多学科合作，我们将努力在第一年的研究中奠定基础，这将有助于改善肉鸡的健康和福利，因此，由于盲肠杆菌感染导致的跛行和瘫痪可以及早发现，这也将有助于减少治疗期间的抗菌药物使用，更成功的治疗结果将有助于防止农民和肉鸡行业遭受巨大的经济损失。在这项雄心勃勃的多管齐下的研究中，将有三个主要组成部分：病原体基因组学；传输/持久性;以及动物行为监测。分离基因组学将有助于提高我们对盲肠杆菌病原体的认识。通过执行详细的分子特征，我们将确定通过从其他细菌，特别是那些生活在同一环境位的细菌转移移动基因而获得的任何遗传元件，这些遗传元件导致这种细菌的毒力增加，并且曾经是共生细菌的倾向导致家禽中的地方病。导致抗微生物药物耐药性的基因与致病变异中存在的关键毒力决定因素的联系，将有助于确定与致病分离物相关的标记，这些标记可用于未来在猪场使用栏侧测试进行快速检测。此外，发现具有来自相同遗传谱系的特定毒力元素的分离株群，将有助于在英国检测与病禽相关的盲肠大肠杆菌类型或克隆。为了确定能够在农场传播和持续存在的环境水库，我们的计划是在五个农场的不同生产周期，对阳性房屋的表面、垃圾和水进行深入采样，并进行阴性对照。盲肠杆菌特异性PCR将有助于确定存在，这将在一个亚群中通过培养进行验证。生存实验将有助于区分盲肠杆菌在家禽房中常见的水、混凝土和塑料中的生存情况，以及我们采样协议的一部分，特别是在接触杀菌剂时。视频传感器和相关的分析工具是密切监测动物行为的极好方法，包括检测任何细微的变化。通过在将进行环境采样的农场和房屋的一个子集上安装传感器，我们将能够使用人工智能来监测鸟群的表现，并识别气候条件、鸟类生长和用水量等参数的偏差。受感染畜群中的偏差将通过兽医检查加以核实，早期行为变化与感染之间的任何相关性将被纳入未来的算法，以帮助及早发现疾病。

Endemic disease such as lameness that may lead to paralysis and death in broiler chickens presents considerable welfare problems, it leads to significant antimicrobial usage and results in substantive economic losses for the broiler industry both within the United Kingdom and worldwide. Enterococcus cecorum, an emerging pathogen, has become associated with infections in affected poultry flocks in the British Broiler Industry. However, little is known about how this commensal has evolved to become a pathogen due to E. cecorum genomics being in its infancy. The environmental reservoir(s) that it occupies which results in apparently sporadic disease occurrence within poultry flocks is also unknown, and no close monitoring is being performed of animal behaviour to determine if any subtle changes occur during the early stages of infection before disease progression and gross physical changes that are associated with lameness becomes apparent. Therefore, in this transformational proof-of concept proposal we aim to fill current knowledge gaps by bringing together a unique and highly skilled project team from diverse backgrounds, gathered through the BBSRC Endemics Livestock Disease Initiative workshops for Priming Partnerships. Through our multi-disciplinary partnership, we will endeavour to lay foundations in the first year of research that will help improve the health and welfare of broiler chickens, so lameness and paralysis due to E. cecorum infection can be detected early, which will also help reduce antimicrobial usage during treatment and more successful treatment outcomes will help prevent large economic losses for farmers and the broiler industry.In this ambitious multi-pronged study, there will be three main components: pathogens genomics; transmission/persistence; and animal behaviour monitoring. Isolate genomics will help advance our understanding of E. cecorum pathogens. By performing detailed molecular characterisation, we will identify any genetic elements that have been acquired via transfer of mobile genes from other bacteria, particularly those living in the same environmental niche, resulting in increased virulence and a propensity of this bacterium, once a commensal, to cause endemic disease in poultry. Linkage of genes that cause resistance to antimicrobials, with key virulence determinants present in pathogenic variants, will help identify markers associated with pathogenic isolates that can be used for rapid detection on farms in future, using pen-side tests. In addition, groups of isolates found to be enriched with particular virulence elements that are from the same genetic lineages, will enable detection of E. cecorum types or clones associated with diseased birds in Great Britain. For identification of environmental reservoirs that enable transmission and persistence on farm, our plan is to perform in-depth sampling of surfaces, litter and water in positive houses and a negative control, at different periods of the production cycle, from five farms. An E. cecorum specific PCR will help identify presence, which will be verified in a subset by culture. Survival experiments will help distinguish how well E. cecorum survives in water, concrete and plastic that are common in poultry houses and part of our sampling protocol, especially upon exposure to biocides. Video sensors and associated analytical tools are an excellent way for monitoring animal behaviour closely, including detecting any subtle changes. By installing sensors on a subset of the farms and houses where environmental sampling will be performed, we will be able to use artificial intelligence to monitor flock performance and identify deviations from parameters such as climatic conditions, bird growth and water consumption. Deviations in infected flocks, will be verified by veterinary inspections and any correlation between early changes in behaviour and infection will be incorporated into future algorithms to help detect disease early.