title: Examining the Role of Transformation in the Acquisition of Resistance and Rescue of Genomes from Oxidative Stress
Creators: name: Proud, CL
Publisher: name: University of Liverpool Repository
Year: 2016

description: The pneumococcus remains a pathogen of global importance due to its ability to circumvent antibiotic and vaccine pressures. For resource poor countries such as Malawi, the threat posed by this pathogen is perhaps the strongest, as access to timely and effective healthcare is limited. Coupled with this, high rates of HIV mean that pneumococcal disease is particularly prevalent in Malawi. The recent rollout of vaccination, anti-retroviral therapy to combat HIV, and increased availability to antimicrobials is helping to control this pathogen. However, recent genetic analyses have already demonstrated the potential for the pneumococcus to circumvent such measures, through vaccine-escape, and antibiotic resistance. The pneumococcus inhabits the nasopharynx where it is thought to recombine with other closely related mitis group species. Such recombination events are thought to have allowed this pathogen to first acquire beta-lactam resistance- a class of antibiotics favoured for the treatment of pneumococcal diseases. Survival within this niche is nonetheless challenging, as it is subject to high levels of attack by charged oxygen particles, termed oxidative stress. Oxidative stress results not only from attack by the host’s immune system, but also from the pneumococci’s metabolism. Such attack has been found to cause a wide variety of genetic lesions in the pneumococcus, and consequently the repair of such damage is likely to be essential for survival. Despite this, the pneumococcus lacks many of the normal repair machineries found in bacteria such as E. coli, and as such some have suggested a role for recombination in this repair process. Detection of genetic damage within collections of clinical pneumococcal isolates in silico indicated deletional damage occurred frequently, and genome-wide. This implied that the damage detected was not a consequence of replication errors, which would be expected to occur clustered close to the origin of replication. Deletion repair was identified as an essential mechanism in order to subjugate the fitness costs associated with such damage in situ. Recombination with siblings (self-repair) appeared to be the dominant force in this process. Attempts to model genetic damage in vitro were however limited, with exogenously delivered hydrogen peroxide appearing to poorly reflect the natural condition. It may therefore be important to consider pneumococci subject to abnormal levels of oxidative stress in clinical settings to better characterise this repair process. Recombination has additionally played a major role in the ability for pneumococci to respond to clinical interventions. The ability for pneumococci, and other mitis group species to circulate globally was found to play an important role in the acquisition of beta-lactam resistance in the Malawian pneumococcal population. Continued epidemiological surveillance of this pathogen will therefore be important in order to assess how this pathogen responds to the current clinical interventions, such as PCV13 vaccination. Although recombination within the mitis group was identified, the interactions between pneumococci and other members of this group remain poorly characterised. Such events however appear infrequent, likely restricted to a subset of the population, such as in infants. Finally, to better elucidate the pathways by which beta-lactam resistance arises clinically; a genome wide approach was taken to identifying resistance associated genes. In addition to indicating novel resistance mechanisms, a role for interspecies recombination within these sites was identified.