Performance of the Xpert Xpress Strep A for detection of Streptococcus pyogenes from pediatric pleural fluids

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ABSTRACT In Canada, Group A streptococcal (GAS) pneumonia is a severe invasive GAS (iGAS) condition reportable to public health for consideration of chemoprophylaxis for close contacts. It is often complicated by parapneumonic effusion. Sterile site culture from pleural fluid is the diagnostic gold standard but is insensitive, particularly given that many patients will have received antibiotics prior to sample collection. Xpert Xpress Strep A (Cepheid, Sunnyvale, CA) is a quantitative real-time (qPCR) assay targeting the speB gene designed to rapidly detect Streptococcus pyogenes from throat swabs. We evaluated its performance compared to bacterial culture for pediatric pleural fluids. A convenience sample of 36 specimens (21 positive, 15 negative) obtained January 2023 to April 2025 was included. Results were compared to a composite reference standard consisting of positive culture and a laboratory-developed (LD) qPCR targeting the spy1258 gene. Limit of detection (LoD) for LD qPCR was determined by testing a dilution series of negative pleural fluids spiked with a predefined concentration (copies/mL) of S. pyogenes ATCC 19615 and using 95% hit rate analysis for Xpert. All 21 positive samples tested (100%) were detected by Xpert and the composite reference standard, while only 8/21 (38%) were culture positive. Xpert demonstrated 100% positive percent agreement, negative percent agreement, and overall categorical agreement (ĸ = 1) with the composite reference standard and individual LD qPCR. There was 64% categorical agreement between Xpert and culture alone (ĸ = 0.3). Xpert was more sensitive for detecting S. pyogenes than culture from pleural fluid. Faster turnaround time shortened the window to optimal therapy, supporting its diagnostic utility. IMPORTANCE Group A streptococcal (GAS) pneumonia, a predominant pathogen in pediatric complicated pneumonia and a severe form of invasive GAS infection, requires prompt diagnosis, both for clinical patient management and identification of close contacts for public health evaluation. Pleural effusion is a common complication. Recovery of GAS from a sterile site like pleural fluid is a key criterion to categorize disease as invasive. However, microbiological yield is often low and may be improved by applying molecular diagnostic techniques. In our study, we demonstrate the utility of Xpert Xpress Strep A for Cepheid GeneXpert for rapid detection of GAS in pediatric pleural fluids. We demonstrated excellent sensitivity with Xpert detecting all 21/21 (100%) positive specimens, compared to culture alone, which was only positive for 8/21 (38%).

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