New research into the effectiveness of vaccines has found that better strategies, including vaccination in adulthood and tailoring vaccines to the strains of bacteria circulating in a community, are required to help reduce overall rates of disease.
Researchers from the University of Helsinki in Finland, Simon Fraser University in Canada and Imperial College London combined genomic data, models of bacterial evolution and machine learning to predict how vaccines could be optimised for specific age groups, geographic regions and communities of bacteria.
The study, published on 3 February in Nature Microbiology, considered in detail the serotype replacement process which implies that when particular strains of Streptococcus pneumoniae are eradicated by a vaccine in childhood, they can be replaced by other strains that could lead to higher rates of disease in adults, and also increase in disease in infants. Using predictive models, the authors concluded that vaccinating people in childhood and adulthood would help reduce overall rates of disease.
“With the power of the latest DNA sequencing technology, we are heading towards a future where large-scale genomic surveillance of major bacterial pathogens is feasible. The approach we describe in this study will play an important role in accelerating future vaccine discovery and design to help reduce rates of disease”, says professor Jukka Corander from the University of Helsinki, the University of Oslo and Wellcome Sanger Institute.
Cause of pneumonia, sepsis and meningitis
S. pneumoniae can cause serious bacterial infections such as pneumonia, sepsis and meningitis – known collectively as invasive pneumococcal disease (IPD). It is estimated that IPD causes around 1.6 million deaths per year worldwide. Infants and the elderly are most at risk.
S. pneumoniae is difficult to target with vaccines because infection can be caused by different serotypes. The common pneumococcal conjugate vaccine targets 13 serotypes (PCV13).
Because there are approximately 90 pneumococcus serotypes around the world, vaccine effectiveness varies between countries depending on which serotypes are present. When serotypes are removed from circulation by a particular vaccine, other serotypes of S. pneumoniae rise to take their place.
In this study, the researchers optimised a computer model to approximate the effect of vaccines targeting different serotype combinations. Analysis of vaccine effectiveness was then carried out on vaccination programme data from around the world.
The much faster approximation method meant it was feasible to intelligently scan through a large subset among the possible vaccine compositions, which there is an astronomic number of. The number of combinations was dependent on the communities of S. pneumoniae present in each location.
Tailored vaccine programmes needed
The results highlight the need for vaccine programmes to be tailored to specific communities of bacteria and to consider vaccination at different ages.
The study also found that disease rates could be reduced by up to 50 per cent by following up infant vaccination with a second vaccine in adulthood. The removal of certain serotypes by childhood vaccines can see them replaced by serotypes better adapted to causing IPD in adults.
The findings coincide with growing alarm at the threat of antimicrobial resistance (AMR) to common medicines, which make infections with bacteria like S. pneumoniae difficult to treat. As such, effective vaccination programmes have an important role to play in reducing rates of disease and the need for antibiotic treatments.
Caroline Colijn, Jukka Corander and Nicholas J. Croucher. Designing ecologically optimized pneumococcal vaccines using population genomics. Nature Microbiology 3.2.2020. DOI 10.1038/s41564-019-0651-y
Professor Jukka Corander
Department of Mathematics and Statistics, University of Helsinki
+358 50 415 5294