Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae

Abstract

Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate at which the organism acquires variation through spontaneous mutations. This higher rate of variation allows the pneumococcus to circumvent the host innate and adaptive immune responses, escape clinical interventions, including antibiotic therapy and vaccine introduction. The rapid influx of whole genome sequence (WGS) data and the advent of novel analysis methods and powerful computational tools for population genetics and evolution studies has transformed our understanding of how genetic recombination drives pneumococcal adaptation and evolution. Here we discuss how genetic recombination has impacted upon the evolution of the pneumococcus.

Keywords: Evolution; Genetic recombination; Streptococcus pneumoniae.

Fig. 1

Schematic representation of genetic recombination events in a subset of PMEN1 ST81 S. pneumoniae genomes from Croucher et al, (2011), Science. (a) A maximum likelihood phylogenetic tree generated using RAxML version 7.0.3 after removing recombination events in the multiple sequence alignment. (b) Location of genetic recombination events in S. pneumoniae genomes. (i) Schematic representation of the sequence features in the S. pneumoniae reference sequence. The genes in some regions with high density of recombination events are shown above the features. (ii) Rectangular matrix showing genomic regions where hypothetical genetic recombination events occurred. Recombination events were inferred as regions with atypically high density of polymorphisms. Each horizontal track beginning from the tips of the phylogeny represents a single aligned whole genome pneumococcal sequence. Green blocks shows the presence of a recombination event that was present in at least one isolate (shared) on the same locus while the red blocks represent unique recombination events (different sizes and locations) that were not shared at a particular locus. (iii) Scale showing the position in the genome. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)