Development of a Prophage Typing System and Analysis of Prophage Carriage in Streptococcus pneumoniae

The frequency of prophage carriage was tested in a collection of 108 clinical isolates of Streptococcus pneumoniae. A PCR-based assay was developed to allow classification of the prophage into the three groups recently identified according to genome comparisons (P. Romero, N. Croucher, N. L. Hiller, F. Z. Hu, G. D. Ehrlich, S. D. Bentley, E. Garcia, and T. J. Mitchell, submitted for publication). Use of the assay showed that more than half of the isolates studied were lysogenic with prophage belonging to group 1 being the most abundant (56%), followed by group 2 (26%) and group 3 (11%). Four polylysogenic strains were identified harboring a group 1 and a group 2 prophage. Interestingly, lysogenic strains were found in 8 out of the 12 internationally distributed, relevant clones of S. pneumoniae contained in our strain collection. The high percentage of clinical pneumococcal isolates harboring prophage strongly suggest an important contribution to the diversification of the genome architecture in this species as well as a role for bacteriophage on the virulence/and or fitness of S. pneumoniae although further studies using a significant number of isolates belonging to the most relevant pneumococcal clones are neede