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 (ϳ3,000) that are represented in the S. pneumoniae population at frequencies of >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.Streptococcus pneumoniae is a gram-positive bacterium commonly found in the nasopharynges of healthy persons, predominantly children. In addition to its commensal form, S. pneumoniae is also a major cause of morbidity and mortality worldwide. S. pneumoniae infection can cause meningitis and bacteremia, as well as many mucosal diseases such as pneumonia, sinusitis, and otitis media (OM). Worldwide, S. pneumoniae infections are estimated to result in 1.1 million deaths a year, predominantly from pneumonia, and even in the United States pneumococcus disease is one of the top 10 causes of death (21). The economic burden associated with S. pneumoniae infections is tremendous, because it is the causative agent for 30 to 50% of OM infections worldwide, and in the United States alone the cost of OM, which is the most prevalent infectious disease among children, is estimated at $5 billion annually (5, 12).S. pneumoniae played a critical role in the demonstration that DNA is the hereditary genetic material. In 1944 Avery and colleagues showed that DNA is the transforming factor identified by Griffith as being capable of making avirulent S. pneumoniae lethal (1). Since then, S. pneumoniae has served as a model organism for the study of bacterial transformation. It contains an inducible system for the...

Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing

“…enterica. These properties are consistent with earlier descriptions of the pan-genomes of these and other species (Hiller et al, 2007;Hogg et al, 2007;Lefebure & Stanhope, 2007;Lindsay et al, 2006;Tettelin et al, 2005;Willenbrock et al, 2007).…”

“…in 205 distributed genes. Thus, microarrays imprinted with all of the genes from a species' distributed genome (Tettelin et al, 2005;Ehrlich et al, 2005;Hogg et al, 2007;Hiller et al, 2007) can be used to obtain accurate typing information that can be used in clinical diagnostics and for epidemiological studies. This type of approach was used when the data from a seven strain Staph.…”

“…The scores for each of the distributed genes were summed and divided by the number of distributed genes to calculate the fraction of distributed genes (FDG) that were the same in both genomes. The distributed gene distance between the two genomes is 12FDG (Hiller et al, 2007). Both distance measures are frequently used.…”

“…influenzae (n513) and S. pneumoniae (n517) (Hiller et al, 2007) has led to the concepts of the 'pangenome' and the distributed genome hypothesis (Ehrlich et al, 2005). More recent studies have extended the concept to E. coli (Willenbrock et al, 2007), Staph.…”

Fratricide in Streptococcus pneumoniae: contributions and role of the cell wall hydrolases CbpD, LytA and LytC

“…It has for instance been firmly established that gene exchange by this mechanism has contributed significantly to the increasing incidence of penicillinresistant S. pneumoniae worldwide (Hakenbeck, 1995;Chi et al, 2007), a development that constitutes a major threat to public health (Jenkins et al, 2008). Gene exchange by natural transformation gives the pneumococcus access to a large gene pool, which it shares with other pneumococcal strains and closely related commensal streptococci (Hiller et al, 2007). Consequently, genes present in the common gene pool that give a selective advantage under certain types of stress (e.g.…”