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

地方性疾病如跛行可能导致肉鸡瘫痪和死亡，这带来了相当大的福利问题，它导致了大量的抗菌剂使用，并导致英国和世界范围内肉鸡产业的重大经济损失。盲肠肠球菌是一种新出现的病原体，已与英国肉鸡业受影响家禽群的感染有关。然而，很少有人知道这种真菌是如何进化成为一种病原体的。cecorum基因组学还处于起步阶段导致家禽群中明显散发性疾病发生的环境水库也是未知的，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的感染早期阶段是否发生任何细微变化。因此，在这个转型的概念验证提案中，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当前的知识空白，这些团队是通过BBSRC地方病牲畜疾病倡议的启动伙伴关系研讨会聚集起来的。通过我们的多学科合作伙伴关系，我们将努力在研究的第一年奠定基础，这将有助于改善肉鸡的健康和福利，使跛行和瘫痪，由于E。盲肠炎感染可以早期发现，这也将有助于减少治疗过程中的抗菌剂使用，更成功的治疗结果将有助于防止农民和肉鸡产业的巨大经济损失。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;传播/持久性;和动物行为监测。分离基因组学将有助于我们进一步了解E.盲肠病原体通过进行详细的分子表征，我们将鉴定通过从其他细菌（特别是生活在相同环境生态位中的细菌）转移移动的基因而获得的任何遗传元件，这些遗传元件导致该细菌的毒力增加，并且一旦成为寄生虫，就有可能引起家禽流行病。导致抗微生物剂耐药性的基因与致病性变异体中存在的关键毒力决定因素之间的联系，将有助于确定与致病性分离株相关的标记，这些标记可用于未来使用围栏试验在农场进行快速检测。此外，发现富含来自相同遗传谱系的特定毒力元件的分离物群，将使得能够检测E。在英国与病鸟有关的cecorum类型或克隆。为了识别能够在农场传播和持久性的环境水库，我们计划在生产周期的不同时期，从五个农场对阳性房屋和阴性对照的表面、垃圾和水进行深入采样。大肠盲肠特异性PCR将有助于识别存在，这将通过培养在子集中进行验证。生存实验将有助于区分E. cecorum在水、混凝土和塑料中存活，这在禽舍中很常见，也是我们采样协议的一部分，特别是在接触杀生物剂后。视频传感器和相关的分析工具是密切监测动物行为的绝佳方式，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子集上安装传感器，我们将能够使用人工智能来监测鸡群的表现，并识别气候条件、鸟类生长和用水量等参数的偏差。受感染鸡群的偏差将通过兽医检查进行验证，行为早期变化与感染之间的任何相关性将被纳入未来的算法，以帮助早期发现疾病。

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.