Capsular polysaccharide (CPS) is a major virulence factor in Streptococcus pneumoniae. CPS gene clusters of S. pneumoniae types 4, 6B, 8, and 18C were sequenced and compared with those of CPS types 1, 2, 14, 19F, 19A, 23F, and 33F. All have the same four genes at the 5 end, encoding proteins thought to be involved in regulation and export. Sequences of these genes can be divided into two classes, and evidence of recombination between them was observed. Next is the gene encoding the transferase for the first step in the synthesis of CPS. The predicted amino acid sequences of these first sugar transferases have multiple transmembrane segments, a feature lacking in other transferases. Sugar pathway genes are located at the 3 end of the gene cluster. Comparison of the four dTDP-L-rhamnose pathway genes (rml genes) of CPS types 1, 2, 6B, 18C, 19F, 19A, and 23F shows that they have the same gene order and are highly conserved. There is a gradient in the nature of the variation of rml genes, the average pairwise difference for those close to the central region being higher than that for those close to the end of the gene cluster and, again, recombination sites can be observed in these genes. This is similar to the situation we observed for rml genes of O-antigen gene clusters of Salmonella enterica. Our data indicate that the conserved first four genes at the 5 ends and the relatively conserved rml genes at the 3 ends of the CPS gene clusters were sites for recombination events involved in forming new forms of CPS. We have also identified wzx and wzy genes for all sequenced CPS gene clusters by use of motifs.Streptococcus pneumoniae is an important human pathogen causing invasive diseases such as pneumonia, bacteremia, and meningitis. Control of pneumococcal diseases is being complicated by the increasing prevalence of antibiotic-resistant strains and the suboptimal clinical efficacy of existing vaccines. The capsular polysaccharide (CPS) of S. pneumoniae is essential for virulence because it protects S. pneumoniae from the nonspecific defence system of the host organism. All fresh isolates from patients with pneumococcal infection are encapsulated, and spontaneous nonencapsulated derivatives of such strains are almost completely avirulent (7).Ninety different CPS types have been identified so far by immunological and chemical techniques (31). Each has a structurally distinct CPS, composed of repeating oligosaccharide units joined by glycosidic linkages. CPS production requires a complex pathway, including synthesis of the activated monosaccharide nucleotide precursors, sequential transfer of each sugar to a lipid carrier to form repeating CPS units, and subsequent polymerization, export, and attachment to the cell surface. The exception to this is type 3 CPS, which has a very simple CPS structure and appears to be synthesized by a processive transferase (6). Classic genetic studies carried out by Austrian et al. (8) demonstrated that the genes encoding CPS biosynthesis are closely linked on the S. pneumoniae chromoso...