301. Clinical impact of a Streptococcus pneumoniae PCR assay on pleural fluid specimens for children with complicated pneumonia
Authors: Ho Erin C , Olson Kaitlin E , Butler Molly , Birkholz Meghan C , Miller Kristen , Jung Sarah A , Asturias Edwin J , Dominguez Samuel R 
Published: January 2025

Abstract

Background
While Streptococcus pneumoniae (Spn) is the predominant pathogen in pediatric complicated community acquired pneumonia (cCAP), it is infrequently recovered by culture-based methods. Without Spn or another pathogen detected, patients often remain on inappropriately broad-spectrum therapy. We studied the real-world clinical impact of a newly implemented, lab developed Spn PCR assay, with target genes lytA, piaB, SP2020, for pleural fluid specimens.

Methods
We compared pathogen detection, antibiotic usage, and outcomes in children hospitalized with cCAP requiring pleural effusion or empyema drainage at Children’s Hospital Colorado between 2016 – 2023. The study population was divided into two diagnostic periods: pre-Spn PCR (October 1, 2016 – July 26, 2022) and post-Spn PCR (July 27, 2022 – September 30, 2023). Kaplan Meier curves and log-rank tests compared time from hospital admission to pathogen detection, optimal therapy, and MRSA therapy discontinuation between periods. Optimal therapy was pre-defined as pathogen-directed therapy or per institutional guidelines (ampicillin in most cases with no pathogen).

Results
Patient characteristics and illness severities were similar across the pre-Spn PCR (N=149) and post-Spn PCR (N=79) periods, and pleural fluid drainage occurred most frequently on hospital day 2 (Table 1). The post-Spn PCR cohort had a higher percentage with any pathogen detected (72.4% vs. 38.5%, p &lt; 0.001), driven by more Spn detections (45.6% vs. 14.1%, p &lt; 0.001) (Table 2). Time to pathogen detection was shorter in the post-Spn PCR period (p &lt; 0.001, Figure 1). Post-Spn PCR patients were more likely to reach optimal antibiotic therapy (84.8% vs. 51.4%, p &lt; 0.001), with shorter median time to optimal therapy (5.0 days vs. 10.3 days, p &lt; 0.001, Figure 2A) and shorter median time to MRSA antibiotic discontinuation (1.5 days vs. 2.5 days, p = 0.03, Figure 2B). There were no differences in hospital length of stay or readmissions (Table 2).

Conclusion
Molecular detection of Spn in pleural fluid of children with cCAP resulted in a significant increase in causative pathogen identification, optimization of antibiotics, and decreased exposure to MRSA antibiotics, demonstrating that PCR is a clinically impactful addition to conventional pneumonia diagnostics.

Disclosures
Molly Butler, PhD, Pfizer: Conference Attendance Sarah A. Jung, PhD, Cobio Diagnostics: Advisor/Consultant|Karius Inc: Advisor/Consultant|Roche Diagnostics: Advisor/Consultant Edwin J. Asturias, MD, BioFire: Grant/Research Support|Hillevax: Advisor/Consultant|Merck: Advisor/Consultant|Moderna: Advisor/Consultant|Pfizer: Grant/Research Support Samuel R. Dominguez, MD, PhD, BIofire Diagnostics: Advisor/Consultant|BIofire Diagnostics: Grant/Research Support|DelveBio: Grant/Research Support|Karius: Advisor/Consultant|Karius: Grant/Research Support|Pfizer: Grant/Research Support