Rapid, whole genome sequencing-based diagnosis of drug-resistant Mycobacterium abscessus complex and new options for treatment

非结核分枝杆菌（NTM）是除结核分枝杆菌复合群和麻风分枝杆菌以外的分枝杆菌物种。它们在环境中无处不在，通常与水，土壤和医院病房隔离。随着免疫功能低下患者（包括HIV感染和血液病患者）以及囊性纤维化和慢性肺部疾病患者数量的增加，NTM作为人类疾病（特别是肺部疾病）的原因的作用变得明显，最近的报告表明全球范围内的增加。特别是，结核分枝杆菌复合体包括一组快速生长的、多药耐药的、非结核分枝杆菌，其引起广谱的皮肤和软组织疾病、中枢神经系统感染、菌血症以及眼部和其他感染。感染M.虽然没有标准的治疗方法，但指南建议将大环内酯类药物与静脉注射的其他抗菌药物联合使用;然而，这种治疗方案已被证明对患者有很大的副作用。此外，药敏试验存在问题，对标准化方法仍没有达成共识，实验室测量的药物敏感性与患者体内观察到的药物活性之间存在重要差异。新的抗分枝杆菌药物（即贝达喹啉，delamanid）和其他用于耐药结核病的化合物（即cloafazimine）没有在参考实验室进行常规抗NTM测试，尽管最近的研究表明一些优秀的活性。全基因组测序（WGS）已应用于广泛的临床场景，英国是世界上第一个在全国范围内率先使用其诊断M。结核病、耐药性检测和分型。这大大缩短了最终诊断的时间，仅在8天内（从数周甚至数月）即可获得一线敏感性数据。然而，NTM长期以来一直在调查中，仍然需要做很多工作，以便通过敏感性测试进行快速诊断。亚种分化的进展使得对M.你有恋母情结例如，与M.红腹叶蝉亚种M.P.红腹叶蝉亚种利什曼原虫对克拉霉素没有诱导性耐药。导致大环内酯类耐药的clarithromycin基因的发现是一个例子，说明快速诊断将使医生能够自信地给予克拉霉素并早期优化治疗。然而，M.红腹叶蝉亚种由于80%的分离株对大环内酯类抗生素耐药，因此大肠埃希氏菌仍然是诊断和治疗的挑战。目前还没有允许快速诊断的测试，并且在最佳抗菌药物和联合治疗方面缺乏共识，加上可用药物的缺乏。因此，进一步研究M.所以需要有一个小的。本研究的主要目的是探讨WGS应用于M。这是一个复杂的系统，特别关注快速检测耐药突变（从而允许早期优化治疗）。次要目的是研究各种化合物对M的抗菌活性。包括抗微生物肽和噬菌体在内的抗菌肽复合物（因此，提供了治疗耐药性的额外选择）。

Nontuberculous mycobacteria (NTM) are mycobacterial species other than the Mycobacterium tuberculosis complex and Mycobacterium leprae. They are ubiquitous in the environment and often isolated from water, soil, and hospital wards. With increasing numbers of immunocompromised patients (including those with HIV infection and haematological disorders), as well as patients with cystic fibrosis and chronic lung disorders, the role of NTM as a cause of human, and in particular pulmonary, disease has become apparent, with recent reports indicating a worldwide increase. In particular, Mycobacterium abscessus complex comprises a group of rapidly growing, multidrug-resistant, nontuberculous mycobacteria that are responsible for a wide spectrum of skin and soft tissue diseases, central nervous system infections, bacteraemia, and ocular and other infections.Current treatment guidelines are based on limited data derived mostly from expert opinion, case series, and few randomized clinical trials. Infections caused by M. abscessus complex are notoriously difficult to treat. Although there is no standard treatment, the guidelines suggest the administration of macrolide-based therapy in combination with other antimicrobial agents administered intravenously; however, this regimen has been shown to have substantial side effects for patients. Additionally, susceptibility testing is problematic and there is still no consensus on a standardized method and there are important discrepancies between drug susceptibility measured in the laboratory and the activity of the drug observed in patients. New antimycobacterial drugs (i.e. bedaquiline, delamanid) and other compounds used in case of drug resistant tuberculosis (i.e. cloafazimine) are not routinely tested against NTM in the reference laboratory, despite recent research studies suggesting some excellent activity. Whole genome sequencing (WGS) has been applied to a wide range of clinical scenarios and England is the first country in the world to pioneer its use on a national scale for the diagnosis of M. tuberculosis, detection of drug resistance, and typing. This has drastically reduced the time to final diagnosis with first line susceptibilities data available in only 8 days (from weeks and sometime months). However, NTM have long been under investigated and much work still needs to be done to allow a rapid diagnosis with susceptibility testing. The advancement of subspecies differentiation has allowed for more effective management of pulmonary disease caused by M. abscessus complex. For example, unlike M. abscessus subsp. abscessus, M. abscessus subsp. massiliense does not have inducible resistance to clarithromycin. The discovery of the erm gene, which is responsible for macrolide resistance, is an example of how rapid diagnosis would enable the physician to confidently administer clarithromycin and optimize treatment early. However, M. abscessus subsp. abscessus still remains both a diagnostic and treatment challenge as 80% of isolates are macrolide resistant. There is no current test to allow a rapid diagnosis and there is a lack of consensus on the optimal antimicrobial agents and combination therapy, combined with the paucity of available drugs. Hence, further research in both rapid diagnosis and treatment options of M. abscessus is needed. The main aim of this research project is to investigate the utility of WGS applied to M. abscessus complex, with a particular focus on rapid detection of drug resistance mutations (thus, allowing early optimization of treatment). The secondary aim is to investigate the antimicrobial activity of various compounds against M. abscessus complex, including anti-microbial peptides and bacteriophages (thus, providing additional options to treat drug resistance).