Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome

Abstract

Streptococcus pneumoniae is a nasopharyngeal commensal that occasionally invades normally sterile sites to cause bloodstream infection and meningitis. Although the pneumococcal population structure and evolutionary genetics are well defined, it is not clear whether pneumococci that cause meningitis are genetically distinct from those that do not. Here, we used whole-genome sequencing of 140 isolates of S. pneumoniae recovered from bloodstream infection (n = 70) and meningitis (n = 70) to compare their genetic contents. By fitting a double-exponential decaying-function model, we show that these isolates share a core of 1,427 genes (95% confidence interval [CI], 1,425 to 1,435 genes) and that there is no difference in the core genome or accessory gene content from these disease manifestations. Gene presence/absence alone therefore does not explain the virulence behavior of pneumococci that reach the meninges. Our analysis, however, supports the requirement of a range of previously described virulence factors and vaccine candidates for both meningitis- and bacteremia-causing pneumococci. This high-resolution view suggests that, despite considerable competency for genetic exchange, all pneumococci are under considerable pressure to retain key components advantageous for colonization and transmission and that these components are essential for access to and survival in sterile sites.

FIG 1

Meningitis- and bacteremia-associated pneumococcal core genomes based on 140 invasive isolates. (A) Box and whisker plot of the number of core gene orthologous clusters observed as the subset of isolates included in the analysis increases, where the subset ranged from 1 to the total number of isolates (n = 140). To generate a subset of isolates, n isolates are randomly selected from the data set. The core genome size is then calculated for n isolates. Each random subset of a given size is generated 100 times. (B) Box and whisker plot of the number of meningitis and bacteremia core gene orthologous clusters observed as the number of isolates included in the analysis increases, where the subset ranged from 1 to the total number of isolates (n = 70). To generate a subset of isolates, n isolates are randomly selected from the data set. The core genome size is then calculated for n isolates. Each random subset of a given size is generated 100 times. (C) Map of the proportion of meningitis-specific core genes in the bacteremia-associated pneumococcal data set (genes present and absent are represented in gray and white, respectively). A list of meningitis-specific proteins is on the x axis, and individual bacteremia-specific isolates with a phylogenetic tree are on the y axis. (D) Map of the proportion of bacteremia-specific genes in the meningitis-associated pneumococcal data set (genes present and absent are represented in gray and white, respectively). A list of bacteremia-specific proteins is on the x axis, and individual meningitis isolates with a phylogenetic tree are on the y axis.

FIG 1

Meningitis- and bacteremia-associated pneumococcal core genomes based on 140 invasive isolates. (A) Box and whisker plot of the number of core gene orthologous clusters observed as the subset of isolates included in the analysis increases, where the subset ranged from 1 to the total number of isolates (n = 140). To generate a subset of isolates, n isolates are randomly selected from the data set. The core genome size is then calculated for n isolates. Each random subset of a given size is generated 100 times. (B) Box and whisker plot of the number of meningitis and bacteremia core gene orthologous clusters observed as the number of isolates included in the analysis increases, where the subset ranged from 1 to the total number of isolates (n = 70). To generate a subset of isolates, n isolates are randomly selected from the data set. The core genome size is then calculated for n isolates. Each random subset of a given size is generated 100 times. (C) Map of the proportion of meningitis-specific core genes in the bacteremia-associated pneumococcal data set (genes present and absent are represented in gray and white, respectively). A list of meningitis-specific proteins is on the x axis, and individual bacteremia-specific isolates with a phylogenetic tree are on the y axis. (D) Map of the proportion of bacteremia-specific genes in the meningitis-associated pneumococcal data set (genes present and absent are represented in gray and white, respectively). A list of bacteremia-specific proteins is on the x axis, and individual meningitis isolates with a phylogenetic tree are on the y axis.

FIG 2

Plot of the number of meningitis and bacteremia isolates represented in each accessory gene cluster. Each circle represents a single gene cluster.