Background: Streptococci, including S. pneumoniae, pyogenes, and intermedius are leading causes of complicated community-acquired pneumonia (cCAP) in children; however, they are infrequently recovered by culture. Pleural fluid PCR assays and plasma microbial cell-free DNA (mcfDNA) sequencing are relatively new and promising culture-independent tests that may increase sensitivity for detecting streptococci in cCAP, but studies on their real-world clinical performance are lacking.
Methods: We compared the diagnostic yields of blood culture, pleural fluid (PF) culture, PF PCR assays, and mcfDNA sequencing for the detection of S. pneumoniae and pyogenes in immunocompetent children hospitalized with cCAP requiring pleural effusion or empyema drainage at Children’s Hospital Colorado from 2022-2024. Additionally, we compared mcfDNA sequencing to conventional cultures for S. intermedius detection in the same cohort.
Results: Across 45 children with cCAP, S. pneumoniae was detected in 0% by blood culture, 4.4% by PF culture, 35.6% by PF PCR and 37.8% by mcfDNA sequencing (p<0.001). S.pyogenes was detected in 4.4% by blood culture, 6.7% by PF culture, and 31.1% by both PF PCR and mcfDNA sequencing (p<0.001). There were no culture-positive cases that were negative by molecular testing. S.intermedius was detected in 0% by blood culture, 4.4% by PF culture, and 8.9% by mcfDNA sequencing (p=0.09). Overall, pathogenic streptococci were detected in 4.4% by blood culture, 15.6% by pleural fluid culture, 67% by available PF PCRs and 78% by mcfDNA sequencing.
Conclusions: Compared to cultures, pleural fluid PCR testing and mcfDNA sequencing had significantly higher real-world diagnostic yield for streptococci in children with cCAP.