Exploring the richness of Mycobacterium bovis strain diversity to decipher the epidemiology of bovine tuberculosis ecology

牛结核病是由牛分枝杆菌引起的一种多物种传染病，给英国乃至全世界的养牛业造成了严重的负担。尽管对牛采取了广泛的控制措施，但牛的疾病仍然没有得到控制，现在英国政府每年花费约1亿GB。疾病的控制由德国食品和药物管理局发布的一项国家战略进行，控制基于对活牛和所有在英国屠宰场屠宰的牛进行例行监测测试。常规监测的基础是使用高度特异但相对不敏感的皮肤测试。当被诊断为感染时，会尝试从皮肤试验阳性的牛身上分离出牛分枝杆菌，这些牛都被屠宰了。大约70%的受感染牛群中可以分离出牛分枝杆菌。被诊断为感染的牛群被置于行动限制之下，然后所有动物都接受重复的皮肤测试，直到没有明显的进一步可检测到的感染。控制的最大挑战之一是，在英格兰和威尔士的高发区，经过限制、测试和释放的所有农场中，有一半在3年内复发。目前尚不清楚这种疾病的负担在多大程度上与牛的持久性或从野生动物，特别是獾的重新引入有关，獾的感染与GB高发区牛的感染密切相关。因此，英国结核病控制中的一个关键问题涉及到牛群的感染源是什么。在个人一级，了解这一点可以采取具体措施防止感染复发。在国家一级，了解持续不断的结核病挑战的来源，可以制定更一般的政策，并针对这种再感染的来源。现代遗传学方法为疾病暴发的法医学评估提供了极大的机会。可以对引起疾病的生物体进行基因测序，以确定它们的来源以及它们与其他疫情和病例的关系。在人类医学中，对导致疾病的细菌进行详细的基因测序现在变得越来越常见，以确定应该采取什么最佳控制措施。新的方法意味着这可以实时完成。在过去的20年里，作为监测的一部分，英国使用传统的遗传方法对引起牛分枝杆菌的细菌进行了例行评估。这些研究将在英国绘制不同基因类型的令人惊讶的有限分布图，从而确定在低发病率地区(通常与牛的迁徙有关)爆发的可能来源；然而，分类不够精细，无法区分当地农场的持久性疾病与从相对较短距离的牛迁徙引入的疫情。我们的工作将使用Defra实验室机构拥有的令人惊叹的牛分枝杆菌分离株文库，并将对2000个精心挑选的追溯样本应用现代全基因组测序方法。我们将使用最近来自Over GB的常规监测样本，特别是对疾病持续存在的农场的监测样本，以评估阻碍我们控制努力的持续存在的不同驱动因素。我们还将使用獾随机控制试验的样本，在该试验中，獾分离株的可用性是无与伦比的，并对牛进行更密集的平行采样，以揭示这两个物种之间复杂的传播动态的更多细节，以便更准确地针对预防牛只未来感染的措施。我们的工作将直接转化为Defra的计划，对高发地区反复感染的农场进行更深入的调查和干预。我们开发的方法将成为研究疾病时采用的常规方法的一部分，就像人类医学一样。

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a multi-species infection that causes a serious burden on the cattle industry in Great Britain (GB), and throughout the world. Despite extensive control measures in cattle, the disease in cattle remains uncontrolled and now costs the UK government around £100 million per year. Control of the disease is governed by a National Strategy, published by Defra.Control is based around routine surveillance testing of living cattle and all those slaughtered in GB slaughterhouses. Routine surveillance is based around the use of a highly specific but relatively insensitive skin test. When infection is diagnosed, attempts are made to isolate M. bovis from skin test positive cattle, which are all slaughtered. M. bovis can be isolated from around 70% of all infected herds. Herds where infection is diagnosed are placed under movement restriction and all animals are then subjected to repeated skin testing until no further detectable infection is evident. One of the great challenges for control is that half of all farms in high incidence areas of England and Wales that are restricted, tested and released have recurrent disease within 3 years. It is unclear how much of this disease burden is associated with persistence in cattle or with reintroduction from wildlife, specifically badgers, whose infection is closely linked with that in cattle in high incidence areas of GB. Thus, a key question in bTB control in Britain relates to what the source of the infection is for herd. At the individual level, knowing this allows for specific measures to be put in place to prevent recurrence of infection. At the national level, understanding the sources of constant bTB challenge, allows for more general policy to be developed and targeted at the sources of this reinfection. Modern genetic methods provide great opportunities for forensic evaluation of outbreaks of diseases. Organisms causing disease can be genetically sequenced to determine their origins and relationships with other outbreaks and cases. Detailed genetic sequencing of bacteria that cause disease is now becoming common in human medicine to determine what optimal controls should be. New methods mean that this can be done in real time. The bacterium that causes bTB, M. bovis, has been evaluated routinely in in GB using traditional genetic methods over the last 20 years as part of surveillance. These studies have the surprisingly restricted distributions of different genetic types to be mapped in Britain - and hence to determine the likely origins of outbreaks that occur in low incidence areas (often associated with cattle movements); however, the classification is not fine grained enough to allow differentiation of local on-farm persistence of disease from that associated with introduction from relatively short distance cattle movements. Our work will use the amazing library of M. bovis isolates held by Defra's laboratory agency and will apply modern whole genome sequencing methods to 2000 carefully selected retrospective samples. We will use samples from recent routine surveillance from over GB, particularly focussing on farms where disease has been persistent, to evaluate the different drivers of persistence that so hamper our control efforts. We will also use samples from the randomised badger control trial where there is unparalleled availability of badger isolates and far more intensively parallel sampled cattle to reveal more details of the complex transmission dynamic between the two species, in order to allow more precise targeting of measures to prevent cattle becoming infected in the future. Our work will translate directly into Defra's plans for more intensive investigation and intervention on farms that repeatedly become infected in high incidence areas. The approaches that we develop will become, as in human medicine, part of the routine approaches taken when investigating disease.