Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage-Specific Divergence and Niche Adaptation

Abstract

Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom's childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types 433 and 698) and conducted comparative genomic analysis on four isolates, paired by Sequence Type (ST) with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of nonsynonymous mutations in pgdA, encoding peptidoglycan N-acetylglucosamine deacetylase A, which was found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Althought no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonization, including bacteriocins, lantibiotics, and toxin--antitoxin systems, were also observed.

Keywords: Streptococcus pneumoniae; genome sequencing; invasive pneumococcal disease.

Fig. 1.—

Pangenome size as defined by shared genes (left) and number of unique genes (right) within the four Streptococcus pneumoniae serotype 22F isolates examined. The dashed blue line represents the core genome size of 1349.

Fig. 2.—

Maximum-likelihood neighbor-joining tree showing phylogenetic placement of the Streptococcus pneumoniae serotype 22F isolates of ST698 (purple) and ST433 (green).

Fig. 3.—

Genome comparisons of four Streptococcus pneumoniae serotype 22F isolates against TIGR4 and ATCC70669 23F. Rings representing ST433 isolates (08 and 3326) are colored green with ST698 isolates (09 and 3298) colored purple. The red labels show regions of gene absences, and gene classifications were derived from TIGR4 annotations in RAST.

Fig. 4.—

Distribution of common virulence genes found in Streptococcus pneumoniae serotype 22F isolates as determined by SRST2. Key: Dark blue, known allele; light blue, novel allele (10% sequence dissimilarity to known allele); black, not identified. Columns are color coded by ST: Green, ST433; purple, ST698.