Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome

Abstract

The distributed-genome hypothesis (DGH) states that pathogenic bacteria possess a supragenome that is much larger than the genome of any single bacterium and that these pathogens utilize genetic recombination and a large, noncore set of genes as a means of diversity generation. We sequenced the genomes of eight nasopharyngeal strains of Streptococcus pneumoniae isolated from pediatric patients with upper respiratory symptoms and performed quantitative genomic analyses among these and nine publicly available pneumococcal strains. Coding sequences from all strains were grouped into 3,170 orthologous gene clusters, of which 1,454 (46%) were conserved among all 17 strains. The majority of the gene clusters, 1,716 (54%), were not found in all strains. Genic differences per strain pair ranged from 35 to 629 orthologous clusters, with each strain's genome containing between 21 and 32% noncore genes. The distribution of the orthologous clusters per genome for the 17 strains was entered into the finite-supragenome model, which predicted that (i) the S. pneumoniae supragenome contains more than 5,000 orthologous clusters and (ii) 99% of the orthologous clusters ( approximately 3,000) that are represented in the S. pneumoniae population at frequencies of >or=0.1 can be identified if 33 representative genomes are sequenced. These extensive genic diversity data support the DGH and provide a basis for understanding the great differences in clinical phenotype associated with various pneumococcal strains. When these findings are taken together with previous studies that demonstrated the presence of a supragenome for Streptococcus agalactiae and Haemophilus influenzae, it appears that the possession of a distributed genome is a common host interaction strategy.

FIG. 1.

Histogram of the number of observed and predicted (by the finite supragenome model) orthologous gene clusters that are present in a given number of genomes. There were 1,454 orthologous clusters observed in all strains (core); 1,140 distributed among more than one strain, but not all; and 576 in only one strain.

FIG. 2.

Dendrogram showing the relationship among 17 S. pneumoniae strains based on orthologous cluster differences.

FIG. 3.

Global comparison of orthologous gene clusters for 17 S. pneumoniae strains. The similarity score corresponds to the total number of orthologous gene clusters shared within each strain pair; the difference score corresponds to the total number of orthologous gene clusters not shared within a strain pairing; and the comparison equals the similarity score minus the difference score. In addition, the number of clusters shared only within a strain pair is noted as pair-unique. If these values are 1, 2, or 3 standard deviations away from the mean of all pairwise comparisons, the boxes are color coded as noted in the key.

FIG. 4.

(A) Plot of the numbers of total and core observed orthologous clusters as a function of the number of strains sequenced. (B) Plot of the number of new observed orthologous clusters as a function of each genome. Numbers were calculated first for two strains and then iteratively for strains added one by one.

FIG. 5.

Predictions using the finite supragenome model. (A) Plot of the numbers of total and core predicted orthologous clusters as functions of the number of strains sequenced. (B) Plot of the number of new predicted orthologous clusters as a function of each genome sequenced. Numbers were calculated first for two strains and then iteratively for strains added one by one.