Pherotypes are driving genetic differentiation within Streptococcus pneumoniae

We studied the distribution of the two major pherotypes in the pneumococcal population and their association with serotype, antimicrobial resistance and genetic lineage. Using multilocus sequence data we evaluated pherotype influence on the dynamics of horizontal gene transfer. We show that pherotype is a clonal property of pneumococci. Standard population genetic analysis and multilocus infinite allele model simulations support the hypothesis that two genetically differentiated populations are defined by the major pherotypes.Severe limitations to gene flow can therefore occur in bacterial species in the absence of geographical barriers and within highly recombinogenic populations. This departure from panmixia can have important consequences for our understanding of the response of pneumococci to human imposed selective pressures such as vaccination and antibiotic use.Horizontal gene transfer and recombination, although recognized as important mechanisms in the evolution of certain phenotypes such as penicillin resistance in both Neisseria meningitidis and Streptococcus pneumoniae, were considered to be rare [1,2]. Full genome sequences and extensive surveys of bacterial populations using multilocus sequence typing (MLST) have challenged this view and established the essential role of horizontal gene transfer and recombination in bacterial evolution, revealing the high frequency of these events [3,4].Streptococcus pneumoniae (pneumococcus) is an important human pathogen, taxonomically recognized as a group within the pneumoniae-mitis-pseudopneumoniae cluster of the Streptococcus genus [5]. The capacity of pneumococci to undergo genetic transformation was recognized early in the study of this bacterium [6] and it was later found that competence presented the intriguing property of being tightly controlled at the population level [7]. Competence was thus one of the first examples of a multicellular bacterial response coordinated by a diffusible signal. These processes