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

牛结核（bTB）由牛分枝杆菌引起，是一种多物种感染，对英国（GB）和全世界的养牛业造成严重负担。尽管对牛采取了广泛的控制措施，牛的疾病仍然不受控制，现在英国政府每年花费约1亿英镑。Defra公布了一项国家战略，控制这种疾病。控制是基于对活牛和所有在英国屠宰场屠宰的牛的常规监测测试。常规监测是基于使用高度特异性但相对不敏感的皮肤试验。一旦确诊感染，就会试图从皮肤试验呈阳性的牛中分离出牛支原体，然后全部宰杀。牛支原体可从约70%的受感染畜群中分离出来。被诊断为感染的畜群受到行动限制，然后对所有动物进行反复皮肤测试，直到没有明显的进一步可检测到的感染。控制的一个巨大挑战是，在英格兰和威尔士的高发病率地区，有一半的农场受到限制，测试和释放，三年内疾病复发。目前尚不清楚这种疾病负担在多大程度上与牛的持续存在或从野生动物（特别是獾）重新引入有关，后者的感染与牛瘟高发地区牛的感染密切相关。因此，在英国控制bTB的一个关键问题是牛群的感染源是什么。在个人层面，了解了这一点，就可以采取具体措施防止感染复发。在国家一级，了解结核分枝杆菌结核病持续挑战的来源，有助于制定更全面的政策，并针对这种再感染的来源。现代遗传方法为疾病暴发的法医鉴定提供了巨大的机会。可以对致病生物体进行基因排序，以确定其起源以及与其他疫情和病例的关系。对致病细菌进行详细的基因测序，现在在人类医学中变得越来越普遍，以确定最佳控制方法。新方法意味着这可以实时完成。过去20年来，作为监测工作的一部分，在GB使用传统遗传方法对引起结核分枝杆菌的细菌牛分枝杆菌进行了常规评估。这些研究惊人地限制了不同基因类型在英国的分布，从而确定在低发病率地区（通常与牛的流动有关）暴发的可能起源；然而，这种分类不够精细，无法区分当地农场内疾病的持久性与相对较近距离牛只运动传入的疾病。我们的工作将使用Defra实验室机构拥有的惊人的牛分枝杆菌分离库，并将采用现代全基因组测序方法对2000个精心挑选的回顾性样本进行测序。我们将使用最近来自英国的常规监测样本，特别是集中在疾病持续存在的农场，以评估阻碍我们控制工作的持续存在的不同驱动因素。我们还将使用随机獾对照试验中的样本，其中獾分离物的可用性无与伦比，并且更密集地平行采样牛，以揭示两个物种之间复杂传播动态的更多细节，以便更精确地针对措施，防止牛在未来被感染。我们的工作将直接转化为Defra的计划，对在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，就像在人类医学中一样，将成为研究疾病时所采取的常规方法的一部分。

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.