Streptococcus suis serotypes characterized by analysis of chaperonin 60 gene sequences

Abstract

Streptococcus suis is an important pathogen of swine which occasionally infects humans as well. There are 35 serotypes known for this organism, and it would be desirable to develop rapid methods methods to identify and differentiate the strains of this species. To that effect, partial chaperonin 60 gene sequences were determined for the 35 serotype reference strains of S. suis. Analysis of a pairwise distance matrix showed that the distances ranged from 0 to 0.275 when values were calculated by the maximum-likelihood method. For five of the strains the distances from serotype 1 were greater than 0.1, and for two of these strains the distances were were more than 0.25, suggesting that they belong to a different species. Most of the nucleotide differences were silent; alignment of protein sequences showed that there were only 11 distinct sequences for the 35 strains under study. The chaperonin 60 gene phylogenetic tree was similar to the previously published tree based on 16S rRNA sequences, and it was also observed that strains with identical chaperonin 60 gene sequences tended to have identical 16S rRNA sequences. The chaperonin 60 gene sequences provided a higher level of discrimination between serotypes than the 16S RNA sequences provided and could form the basis for a diagnostic protocol.

FIG. 1

Phylogenetic consensus tree for S. suis serotype chaperonin 60 gene partial nucleotide sequences obtained by the neighbor-joining method (300 bootstraps). Pairwise distance matrices were calculated by the maximum-likelihood option of dnadist within PHYLIP (7). The numbers at the nodes indicate the numbers of occurrences of the branching patterns in 300 runs. The horizontal lengths of the branches are proportional to the distances between sequences. The strains used and GenBank accession numbers for the chaperonin 60 gene sequences are listed in Table 1. sero, serotype.

FIG. 2

Phylogenetic consensus tree for Streptococcus chaperonin 60 gene partial nucleotide sequences obtained by the neighbor-joining method (300 bootstraps). Pairwise distance matrices were calculated by the maximum-likelihood option of dnadist within the PHYLIP package (7). The numbers at the nodes indicate the numbers of occurrences of the branching patterns in 300 runs. The horizontal lengths of the branches are proportional to the distances between sequences. The strains used and sequence accession numbers are listed in Table 1. Representative serotypes for the four clusters of S. suis serotypes are enclosed in boxes. sero, serotype.

FIG. 3

Phylogenetic consensus tree for representative chaperonin 60 S. suis peptide sequences obtained by the neighbor-joining method (300 bootstraps). Distances were calculated by the PAM method within the protdist software (7). The numbers at the nodes indicate the numbers of occurrences of the branching patterns in 300 runs. The horizontal lengths of the branches are proportional to the distances between sequences. The strains used and sequence accession numbers are listed in Table 1.

FIG. 4

Distribution of chaperonin 60 gene (cpn60) and 16S rRNA pairwise DNA sequence identities (4) for 35 S. suis serotypes. The total number of pairwise comparisons used for each gene is 595.