Streptococcus pneumoniae infections remain the major cause of pneumonia, meningitis and otitis in many countries. The reservoir of S. pneumoniae is the human nasopharynx. The pneumococci are extremely diverse. This diversity was first evidenced by serotyping of their capsular polysaccharides: The pneumococci are resolved into more than 90 serotypes. However, 16 serotypes cause approximately 90% of invasive disease worldwide. The pneumococcal population evolves more by recombination than by mutations because of horizontal gene transfer by transformation. One serotype can belong to different genotypes, and one genotype can include different serotypes because of capsular switching. Two medical interventions changed the epidemiology ofpneumococcus infections in the world: the use of antibiotics and, more recently, the use of conjugate vaccines. We need molecular tools to track the emergence and the spread of resistant, hypervirulent or non-vaccine types clones.

Different DNA-based methods utilize genetic polymorphism. Pulsed-Field Gel Electrophoresis analysis and Multiple Loci Sequence Typing (MLST) are the most frequently used genotyping techniques. for S. pneumoniae. An MLST typing system was described by Enright et al. together with an online identification page at http://www.mlst.net. The rep-PCR or BOX PCR assay was described in 1996 by van Belkum. The different techniques have been compared in several studies. Other methods use the sequencing of PCR product such as the gal U gene, or the PCR restriction profile of the cpsAcpsB genes. Although some of these techniques have proven their capacity to discriminate efficiently among the multiple serotypes, the data are not always reproducible between different laboratories, some may not be amenable to the making of international databases, or they are time consuming and expensive. Polymorphic tandem repeat sequencesalso called Variable Number of Tandem Repeats (VNTR) are an interesting class of genetic markers. Multiple alleles may be present at a single locus, and size differences are easily resolved by electrophoresis of PCR products. Tandem-repeat typing has proved to be highly appropriate for the typing of pathogenic bacterial species, including species with a very high genetic homogeneity such as the Mycobacterium tuberculosis complex, Bacillus anthracis and Yersinia pestis. The availability of genome sequence data from different S. pneumoniae strains greatly facilitated the search for polymorphic DNA sequences.

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