Developing novel therapies for Mycobacterium abscessus

Mycobacterium abscessus (M. abscessus) is a rapid growing non-tuberculous mycobacteria (NTM) that is increasingly recognised as a major pathogen owing to its inherent resistance to a wide range of the currently available antibiotic therapies. In particular, it causes problems in patients with Cystic Fibrosis (CF) with evidence of marked inflammation, frequent infective exacerbations and an accelerated decline in lung function. Current treatment outcomes are extremely poor. There is therefore an urgent need to understand how M. abscessus resists killing by existing antibiotics and to find new treatments. I have attempted to address these issues in this thesis, particularly relating to the development of novel treatment regimens and antimicrobial agents. I first analysed the treatment outcomes for the CF patients infected with M. abscessus at the Royal Papworth Hospital to examine whether specific antibiotic combinations were associated with better treatment outcomes and could therefore form the basis for a novel treatment regimen. I showed that, despite expert care, the rates of achieving a sustained culture conversion following often prolonged treatment was around 30%, matching the results available from the limited published data. I could find no strong evidence that particular antibiotic combinations were better, further motivating my search for new treatment strategies. I then designed a novel regimen of existing antibiotics (based on synchronous targeting of cell wall, protein synthesis and cellular energetics) to use in CF patients with either treatment-naïve or refractory disease. I demonstrated good efficacy in vitro against a range of clinical isolates of M. abscessus. Subsequent GWAS analysis revealed several potential resistance pathways, including a variety of metabolic pathways and membrane transport systems, which could be used to stratify patients in a future clinical trial. I also developed and evaluated a novel highly effective formulation of acidified nitrite as a new nebulised antimicrobial therapy for M. abscessus which has been shown to have in vivo activity and is currently being evaluated in a clinical trial. Finally, I have developed a method using ultra-performance liquid chromatography to detect intracellular permeability of compounds to support fragment-based antibiotic discovery. I screened a library of 960 fragments to assess for permeation into M. abscessus. Machine learning was then used to generate a predictive algorithm for bacterial permeation that can be used in future fragment-based campaigns.