Using bioinformatics to determine the strain structure of Streptococcus pneumoniae by a multilocus sequence typing (MLST) approach
Streptococcus pneumoniae infection can cause a range of symptoms, and can lead to otitis media and menigitis, as well as to pneumonia. Infection is a cause of morbidity and mortality in people of all ages, but it is a particular problem in the elderly and in children. In developing countries infection of young children is common, with up to 1 million deaths each year.
Multi-Locus Sequence Typing (MLST) is a method for the characterisation of isolates of bacterial species. Usually seven housekeeping genes are chosen. These genes encode essential metabolic enzymes, and so are likely to be under strong stabilising selection. Internal fragments of the genes are sequenced and each gene is assigned as an allele. Each isolate is characterised by a combination of alleles, giving an allelic profile, or sequence type (ST) isolate.
The aim of this study was to establish the strain structure of pneumococci in circulation in the pre-vaccination period in a rural population in sub-Saharan Africa. The specific objectives were to :
- determine the sequence types, and hence the strain structure, of pneumococci in circulation in the population before the introduction of a vaccine;
- compare the circulating sequence types with those that are already determined from other parts of the world, and are stored in a database accessible to the public.
Further work
Following the successful completion of the project, Ben has registered for a PhD. He will continue working on genomic analysis of Streptococcus pneumonia, but using data from next generation sequencers.