ARGENT: ARgentinian GEnomics for Tuberculosis

传染病(每年100多万人)和耐药感染(约50万人/年)造成死亡的最大原因是引起结核病的结核分枝杆菌。由耐药感染引起的死亡中约有三分之一是由结核病引起的。这可能是世界面临的最大单一的传染性公共卫生威胁，2017年全球有160万人死于结核病(https://www.who.int/gho/tb/en/).由于耐药性导致治疗失败，护理标准是检测患者的细菌样本，以确定哪些药物可能有效。以培养为基础的黄金标准方法速度慢(需要数周时间)且费用昂贵，因此许多国家使用基于DNA扩增的快速(数小时)测试来检测对利福平的耐药性，利福平是非耐药结核病的推荐治疗方法。如果他们看到利福平耐药，他们务实地认为样本也对异烟肼耐药，因此产生多药耐药(MDR)。如果这一假设是错误的，患者将接受18个月的不适当治疗，并出现残酷的副作用。还有一种选择：(通常)从患者的痰中分离导致感染的细菌，然后通过一种称为全基因组测序的过程对细菌DNA进行解码。由于耐药性是由细菌中DNA序列(突变)的特定变化引起的，测序提供了描述细菌耐药性图谱的全面输出。抗药性的途径有很多，对整个基因组进行解码可以获得所有这些突变。全基因组测序的第二个好处是，密切相关的细菌具有非常相似的DNA，如果一个人感染另一个人，他们的细菌菌株就是密切相关的。因此，人们可以破译许多患者结核病样本中的突变模式--这提供了可操作的信息，可以指导疫情的预防和管理。挑战是将全基因组测序转化为在公共卫生实验室或医院运行的生产系统，具有可接受的错误率和对医生、护士和公共卫生从业者有意义的输出。世界上唯一采用全基因组测序技术进行结核病诊断、患者管理和疫情监测的国家是英国。通过GCRF资助的CABANA项目，EMBL-EBI正在与阿根廷国家参考实验室合作，该实验室负责确认阿根廷和邻国的所有结核病诊断。这个名为银色的项目将实现两个目标。首先，它将使我们能够与处理结核病病例的专家密切合作，在阿根廷开展用于诊断和管理结核病的全基因组测序的可行性研究。将这种服务引入日常使用需要非常仔细的验证和认可，这超出了本项目的范围。然而，通过特别引入经过严格测试的软件工作流程，并在英国被开发为专门设计用于与其他国家共享的经认可的工作流程。其次，该项目将建立一个全球开放的网络平台(Mykrobe Atlas)，包含全球所有(50000)结核病基因组，允许用户上传自己的样本，并立即将他们的样本与以前的样本进行比较。由于几个国家有法律障碍阻止共享病原体序列数据，一个关键的子研究将是试验一种中心辐射式模式，允许一个国家参与Atlas，同时将其原始序列数据保留在本国。通过由阿根廷实验室领导的与拉丁美洲其他国家的超国家网络，我们将与该地区的其他国家实验室以及非洲和亚洲那些疾病负担最重的国家分享我们的学习。

The biggest cause of deaths due to infectious disease (over 1 million/year) and drug-resistant infections (~0.5 million/year) is the bacterium Mycobacterium tuberculosis, which causes tuberculosis (TB). About one third of deaths caused by drug-resistant infections are due to TB. This is possibly the single biggest infectious public health threat the world faces, with 1.6 million reported deaths globally due to TB in 2017 (https://www.who.int/gho/tb/en/). As drug resistance leads to treatment failure, the standard-of-care is to test a bacterial sample from a patient, to determine which drugs are likely to be effective. The gold standard culture-based approach is slow (taking many weeks) and expensive, so many countries use a fast (hours) test based on DNA amplification to detect resistance to rifampicin, the recommended treatment for non-drug-resistant TB. If they see resistance to rifampicin they pragmatically assume the sample is also resistant to isoniazid, and therefore multi-drug resistant (MDR). When this assumption is wrong, the patient is being subjected to 18 months of inappropriate treatment with brutal side-effects.There is an alternative: the bacteria causing the infection can be isolated from (usually) the sputum of a patient, and the bacterial DNA decoded by a process called whole genome sequencing. Because drug resistance is caused by specific changes to the DNA sequence (mutations) in the bacterium, sequencing provides a comprehensive output describing the resistance profile of the bacteria. There are many roads to drug resistance, and decoding the whole genome allows access to all of these mutations. A secondary benefit to whole-genome sequencing is that closely related bacteria have very similar DNA, and if one person infects another, their bacterial strains are closely related. Thus one can decode the mutation patterns in TB samples from many patients - this provides actionable information that can direct the prevention and management of outbreaks.The challenge is turning whole-genome sequencing into a production system that runs in a public health lab or hospital, with acceptable error rates and outputs that make sense to doctors, nurses and public health practitioners. The only country in the world to have adopted whole genome sequencing for TB diagnosis, patient management and outbreak surveillance is the UK. Through the GCRF-funded CABANA-project, EMBL-EBI is collaborating with the Argentinian National Reference Lab, which is responsible for confirming all the TB diagnoses in Argentina and in neighbouring countries. This project, named ARGENT, will achieve two things. First, it will enable us to perform a feasibility study of whole-genome sequencing for diagnosis and management of TB in Argentina, working closely with the experts dealing with the TB cases. Introduction of such a service into routine use requires very careful validation and accreditation, which is beyond the scope of this project. However, by specifically introducing a software workflow which is heavily tested, and being developed in the UK into an accredited workflow specifically designed to be shared with other countries. Second, the project will build a global, open, web platform (Mykrobe Atlas) incorporating all (>50000) global TB genomes, allowing users to upload their own samples and immediately compare theirs with all that have gone before. Since several countries have legal blocks preventing sharing of pathogen sequence data, a key sub-study will be to trial a hub-and-spoke model that allows a country to participate in Atlas while retaining their raw sequence data in country.Through the supranational network with other countries in Latin America, led by the Argentinian lab, we will share our learning with other national labs in the region, and also in those countries with the greatest burden of disease - in Africa and Asia.