Identification of phage DNA, common insertion sites and their effect on genes within S.pneumoniae
Invasive S.pneumoniae strains are known to cause bacterial pneumonia, bacteremia, meningitis and otitis media and are responsible for the deaths of over a million children annually. Attempts to vaccinate the population has had mixed success due to mutation of the strains to resist the vaccine and antibiotic treatments. One source of these mutations is the insertion of phage DNA into the S.pneumoniae genome. Prophage DNA can provide benefits to infected bacteria such as antibiotic resistance. The insertion of phage DNA can be in common insertion sites or completely random, both of which can cause mutation but in different ways.
This study seeks to find if there are any common insertion sites across different strains of S.pneumoniae and discover genes that undergo frequent mutation due to phages and if these mutations can be linked to virulence of the strains. Using DNA available online via genbank as well as novel S.Pneumoniae sequences provided by collaborators in the faculty of medicine, phage DNA will be compared to bacterial DNA via BLAST searches. The data from this will then be analysed to attempt to discover common insertion sites and the genes that these may be mutating.
Visualisation and data handling methods: Database
Programming languages and libraries: Python