Evolutionary Genomics of Cystic Fibrosis and Nosocomial Pathogens of the Mycobacterium abscessus species complex

The $\textit{Mycobacterium abscessus}$ species complex (MABSC) consists of three subspecies, $\textit{M. a. abscessus}$, $\textit{M. a. massiliense}$ and $\textit{M. a. bolletii}$. All three of these subspecies are capable of causing opportunistic pulmonary and skin and soft tissue infections in immunocompromised individuals. Infections caused by the MABSC are particularly serious in people with underlying lung conditions such as Cystic Fibrosis (CF) as these organisms are highly antibiotic resistant and the currently available treatment is toxic. This has resulted in treatment of MABSC infections failing in up to 50% of cases. Given the increasing prevalence globally of infections caused by the MABSC, particularly in individuals with CF, there is increased urgency to improve the treatment available for MABSC infections. The overall aim of this project was to use genomic analyses to increase our understanding of how the MABSC has evolved to become an opportunistic pathogen, which in turn could potentially uncover promising targets for the development of novel antibiotics. Genomic analysis of the MABSC has already shown that lineages of the MABSC are capable of indirect person to person transmission and the extent to which transmission contributed to the increasing prevalence of MABSC in people with CF became evident when the MABSC global population structure was determined. This showed that 70% of the MABSC isolates from people with CF were attributed to lineages made up of densely clustered isolates, where acquisition via indirect person-to-person transmission, as opposed to from the environment, was more likely. This thesis used population genomic approaches to i) investigate the genetic factors that drove the emergence of the most prevalent MABSC lineages, ii) look for evidence of convergence after the clonal expansion of these lineages to understand how the MABSC was continuing to adapt and spread amongst people with CF and iii) to examine the within host evolution of these pathogens to uncover how these environmental organisms were adapting to the CF lung. This thesis also used whole genome sequencing to explore the largest known outbreak of MABSC infections, a post-surgical wound infection epidemic in Brazil. Through this research the emergence of the most prevalent MABSC lineages were found to be driven by increased opportunity, probably due to the increased number of people with CF surviving longer, as opposed to the acquisition of a common genetic determinant. Not enough signal was detected after the clonal expansion of the most prevalent MABSC lineages to come to strong conclusions about genetic factors driving their continuing expansion, but strong evidence of convergent evolution was detected between MABSC isolates evolving over time within the host. The MABSC was shown to be potentially using a similar central regulatory network in response to environmental cues from the phagosome to that of $\textit{M. tuberculosis}$. The investigation into the epidemic of post-surgical wound infections in Brazil showed that a single $\textit{M. a. massiliense}$ lineage was introduced into Brazil just prior to the initial outbreak and that this lineage subsequently spread, through several waves of transmission, to multiple cities in geographically distant areas of Brazil. This highlighted how the MABSC was capable of long distance transmission and emphasised the potential of the MABSC as a nosocomial pathogen capable of causing large scale outbreaks