Surprising pattern in bacterial evolution

Rather than mutations in core genes, the frequency of accessory genes in bacterial populations regulates the reproductive capacity of bacteria and their ability to spread from one host to another.

Scientists have found a new mechanism regulating the evolution of bacterial populations and this discovery appears as one of the most significant findings about bacterial evolution in the recent years. Contrary to previous beliefs, the reproductive capacity of bacteria and their ability to spread from host to host is not primarily regulated by mutations in their core genome, but by the frequency of so-called accessory genes in the whole population.

Professor Jukka Corander and Dr Nicholas Croucher published their new findings in Nature Ecology & Evolution Advance Online Publication (AOP) on 16 October 2017. They coordinated a project focusing on the study of the evolution of pneumococci based on cohort genome data from several countries.

– Our new simulation model describing the pressure of selection in population evolution can be used for designing better bacterial vaccines, for example, to maximise their effect, says Jukka Corander.

First step: sequencing the pneumococcal genome

The pneumococcus is a common cause of pneumonia and other infections, especially in small children and the elderly. Pneumococci have been found to contain a lot of genetic variation, but it has remained unclear exactly which evolutionary forces maintain this variation.

To analyse the evolution of bacteria, Jukka Corander and Nicholas Croucher, along with their teams, studied the whole genomes of pneumococci from samples covering almost a decade and from several countries.

Next step: develop predictive evolutionary computer simulation

Together, Corander and Croucher developed an evolutionary computer-simulation model, with which they were able to predict accurately how the pneumococcal populations in different countries would react when a pneumococcal vaccine was deployed.

The mechanism coded in the simulation model is akin to research findings in animal populations, which have shown that each individual’s capacity for reproduction depends on how common a certain of its features is in the surrounding population.

– One example of this is how a harmless species may have an appearance that mimics that of a poisonous species, Corander says.

– If the poisonous species is common enough in a certain area, the harmless species has good protection in the same area, because predators have learned to avoid the poisonous kind.

Among the pneumococci, this selection pressure acts inversely so that, the rarer a certain accessory gene in the genome is, the more it benefits the individual pneumococcus trying to spread through the population.

Quantifying magnitude of selection pressure on auxiliary genes with an inference algorithm

Using the new generation of inference algorithms developed by Professor Corander’s research group and the Finnish Academy COIN centre of excellence, the scientists were able to quantify the magnitude of the selection pressure of the auxiliary genes. The results took them by surprise.

The selection pressure was almost identical in all populations, though the bacterial strains had very different genomes and the cohorts had been gathered in different ways: some from healthy carriage in young children and some from unvaccinated adults suffering from meningitis.

– We were totally surprised by our initial findings. On the basis of previous research, we didn’t expect that this pattern would be present, and that the negative frequency-dependent selection pressure would dominate what would happen in the populations to such an extent.

The general evolutionary mechanism is supported also by recent E.coli data

The scientists are convinced that this is a common evolutionary mechanism that affects many species of bacteria, if they have a large accessory genomes and experience frequent horizontal gene transfer.

This hypothesis is strongly supported by the stable evolutionary trajectories detected recently in a nationwide E.coli bacteremia cohort in Great Britain.

Reference

Corander et al. Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nature Ecology & Evolution.

More details

Jukka Corander works in the Faculty of Medicine at the University of Oslo, at the Sanger Institute in Cambridge, and in Helsinki Institute for Information Technology,  a joint venture of the University of Helsinki and Aalto University. Evolutive epidemiology is one of Corander’s central topics in his new ERC Advanced Grant project.

Contact details:

Jukka Corander, 050 415 5294, jukka.corander@helsinki.fi