Online Abstracts Basic Sciences - Genomics and Transmission A3 Genomics and Transmission



Streptococcus pneumoniae is the most common cause of pneumonia in children, including empyema, a severe complication. Over 90 serotypes of pneumococcus exist, but only a subset cause empyema. Virulence determinants of empyema remain largely unknown.


For viable pneumococcal isolates from invasive pneumococcal disease at Primary Children’s Hospital (Salt Lake City, UT) from 1996-2018, we performed Illumina sequencing, de novo genome assembly (SPADES), annotation (PROKKA), and serotyping via Quelling and in silico (SeroBA). ROARY was used for pan-genome assembly, and SCOARY for microbial GWAS. Maximum likelihood phylogeny was calculated using RAxML.


354 pneumococcal isolates were analyzed from 37 serotypes and a spectrum of phenotypes including pneumonia (n=84), empyema (n=54), CNS infection (n=50), and isolated bacteremia (n=68). 6462 genes comprised the pneumococcal pan-genome, with only 23% present in 99% of isolates. Serotype and empyema phenotype clustered roughly by phylogeny. Specific capsule synthesis and diverse metabolic regulatory genes were statistically correlated with the empyema phenotype.


Genetic clustering of empyema isolates within and across serotypes supports genetic determinants of virulence. Altered metabolic regulation may confer optimal fitness for pleural disease. Further validation and characterization of critical determinants of empyema will inform future efforts at prevention and treatment.