Heterogeneity among estimates of the core genome and pan-genome in different pneumococcal populations

Abstract

BackgroundUnderstanding the structure of a bacterial population is essential in order to understand bacterial evolution, or which genetic lineages cause disease, or the consequences of perturbations to the bacterial population. Estimating the core genome, the genes common to all or nearly all strains of a species, is an essential component of such analyses. The size and composition of the core genome varies by dataset, but our hypothesis was that variation between different collections of the same bacterial species should be minimal. To test this, the genome sequences of 3,121 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (USA) and Maela (Thailand) were analysed.ResultsThe analyses revealed a ‘supercore’ genome (genes shared by all 3,121 pneumococci) of only 303 genes, although 461 additional core genes were shared by pneumococci from Reykjavik, Southampton and Boston. Overall, the size and composition of the core genomes and pan-genomes among pneumococci recovered in Reykjavik, Southampton and Boston were very similar, but pneumococci from Maela were distinctly different. Inspection of the pan-genome of Maela pneumococci revealed several >25 Kb sequence regions that were homologous to genomic regions found in other bacterial species.ConclusionsSome subsets of the global pneumococcal population are highly heterogeneous and thus our hypothesis was rejected. This is an essential point of consideration before generalising the findings from a single dataset to the wider pneumococcal population.

Puzzling Over the Pneumococcal Pangenome

“…In this manner, about three quarters of pneumococcal genes are differentially distributed across strains (Figure 1 ). Notably, in a study of isolates from the Maela refugee camp in Thailand, the pangenome structure was distinct from other studies: the pangenome was estimated at approximately 13,000 orthologous clusters and the core at approximately 400 ( Tonder et al, 2017 ).…”

“…Over twenty percent of the coding sequences of any single pneumococcal isolate are not encoded in all strains, but instead are part of an accessory genome unevenly distributed across isolates of this species (Figure 1 ; Hiller et al, 2007 ; Donati et al, 2010 ). The pneumococcal core genome is estimated to encode 500–1100 clusters of orthologues ( Donati et al, 2010 ; Croucher et al, 2013a ; Gladstone et al, 2015 ; Tonder et al, 2017 ). In contrast, the pneumococcal pangenome is estimated to encode 5000–7000 clusters of orthologues (see Table 1 for definitions) ( Donati et al, 2010 ; Croucher et al, 2013a ; Gladstone et al, 2015 ; Tonder et al, 2017 ).…”

“…The pneumococcal core genome is estimated to encode 500–1100 clusters of orthologues ( Donati et al, 2010 ; Croucher et al, 2013a ; Gladstone et al, 2015 ; Tonder et al, 2017 ). In contrast, the pneumococcal pangenome is estimated to encode 5000–7000 clusters of orthologues (see Table 1 for definitions) ( Donati et al, 2010 ; Croucher et al, 2013a ; Gladstone et al, 2015 ; Tonder et al, 2017 ). In this manner, about three quarters of pneumococcal genes are differentially distributed across strains (Figure 1 ).…”

Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions

“…We thank Reza Rezaei Javan for his analysis of the two bacteriophage sequences. A pre-print version of this article was published in bioRxiv (van Tonder et al, 2017).…”

Discovery and description of a new serogroup 7 Streptococcus pneumoniae serotype, 7D, and structural analysis of 7C and 7D

“…However, many additional novel serotypes have been proposed based on genotypic analysis [4,5] or reaction with monoclonal antibodies [6]. Some of the described novel variants based on genotypic differences actually produce no difference in the structure of the polysaccharide, for example the putative serotype 6E which in fact produces a polysaccharide identical to serotype 6B [7], and the genetic variant of 23B which, although it has low sequence homology in the capsular operon and is from an entirely different genetic lineage to the originally described 23B, produces an identical polysaccharide and is therefore the same phenotypic serotype [8].…”