Comparative genomics for identification of clone-specific sequence blocks in Streptococcus pneumoniae

The partial genome sequences of a serotype 3 and a serotype 2 pneumococcal strain were compared to the complete type 4 pneumococcal genome. Over 500 0 00 and 150 000 base pairs of the partial genome data, obtained from publish ed patents, were analysed respectively. Global alignment showed that nearly the whole genome is highly conserved in accordance with data of multilocus sequence typing of housekeeping genes. The search for clone-specific genes revealed 17 new open reading frames in the type 3 strain, while no new ope n reading Frame was detected in the type 2 strain. Allelic variation of gen es was restricted by the use of crude sequence data, but still permitted id entification of some new alleles and the observation that all surface prote ins present in the partial genome data were highly conserved. In both strai ns we observed also a variety of chromosomal rearrangements and variations due to mobile genetic elements. All together, this comparative genomic appr oach gives a genome-based overview of strain relatedness and a prospective on what could be expected when sequencing other pneumococcal strains. (C) 2 001 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.