Understanding Vaccine Impact with Genomics
Whole genome sequencing and modelling of Streptococcus pneumoniae has revealed how modern vaccines have eliminated harmful strains from the population and how surviving strains compete against one another afterwards. The research, published in Nature Ecology and Evolution yesterday, used a new algorithm developed by first author Jukka Corander to study genomic data from bacterial populations in the UK, the USA, and the Netherlands.
S. pneumoniae are a very common species of bacteria and primarily exist harmlessly at the back of the naval cavity in humans. However, the bacteria can spread to other parts of the body and multiply, resulting in the development of pneumococcal diseases like pneumonia, meningitis, and blood infections. To protect patients from these potentially lethal diseases, the UK has introduced two vaccines for children in the last 11 years: the 7-valent vaccine in 2006, and the 13-valent vaccine which replaced it in 2010. Correspondingly, the UK saw a decrease in the occurrences of pneumococcal diseases.
Despite the decrease in the number of harmful strains of S. pneumoniae, however, research has shown that the level of bacteria at the back of the nasal cavity has remained constant. To better understand how this had happened, the team studied 3 large genomic collections from the Wellcome Trust Sanger Institute. The collections gave the team data on the genomic sequences (and, in particular, gene frequency) of S. pneumoniae in the UK, the USA, and the Netherlands before and after vaccination programmes were introduced.
The team found that while different strains of the bacteria were dominant in the different regions, all three populations exhibited similar gene frequencies. The same results were found when the team compared sequence data from before the vaccines were introduced, to data from several years later when the programmes had been implemented.
The algorithm that they used determined that it was highly unlikely the results were due to chance, leading the team to believe that selection pressures were guiding bacterial development. Importantly, they also noted that certain genetic variations were favoured when they were rarer in the population, indicating that they were subject to negative frequency-dependent selection.
This research is an important insight into how bacterial ecology can affect the impact of clinical treatments, such as vaccines, as well as how modern medicines can alter the natural gene pool of bacterial populations. With ‘superbugs’ becoming more and more of a threat to public health, research like this may be important for the development of novel treatment approaches in the future.