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Performance of the Xpert Xpress Strep A for detection of Streptococcus pyogenes from pediatric pleural fluids
Geneviève Amaral1, Vijay J Gadkar1,2, Abdulrahman Almodahka1
1Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
Insights
The Xpert Xpress Strep A test accurately detects Group A Streptococcus in pediatric pleural fluid, outperforming traditional culture methods. This rapid molecular test aids in timely diagnosis and management of invasive Group A Streptococcus infections.
Area of Science:
- Microbiology
- Infectious Diseases
- Molecular Diagnostics
Background:
- Group A Streptococcus (GAS) pneumonia, a severe invasive GAS (iGAS) infection, often presents with parapneumonic effusion in children.
- Traditional culture of pleural fluid for GAS diagnosis has low sensitivity, especially after antibiotic administration.
- Rapid and accurate diagnostic methods are crucial for patient management and public health interventions.
Purpose of the Study:
- To evaluate the performance of the Xpert Xpress Strep A quantitative real-time PCR (qPCR) assay for detecting *Streptococcus pyogenes* in pediatric pleural fluid specimens.
- To compare the diagnostic accuracy of Xpert Xpress Strep A against bacterial culture and a laboratory-developed qPCR assay.
- To assess the clinical utility of Xpert Xpress Strep A in improving the speed of diagnosis for invasive GAS pneumonia.
Main Methods:
- A convenience sample of 36 pediatric pleural fluid specimens (21 positive, 15 negative) were tested.
- Performance of Xpert Xpress Strep A was compared to bacterial culture.
- A composite reference standard, including positive culture and a laboratory-developed qPCR targeting the *spy1258* gene, was used for validation.
- Limit of detection for the laboratory-developed qPCR was determined using a dilution series.
Main Results:
- Xpert Xpress Strep A detected 100% (21/21) of positive samples, significantly outperforming culture, which identified only 38% (8/21).
- The assay demonstrated 100% positive and negative percent agreement with the composite reference standard (ĸ = 1).
- Xpert Xpress Strep A showed superior sensitivity compared to culture alone (64% agreement, ĸ = 0.3).
Conclusions:
- Xpert Xpress Strep A is a highly sensitive and accurate molecular diagnostic tool for detecting *Streptococcus pyogenes* in pediatric pleural fluids.
- The rapid turnaround time of Xpert Xpress Strep A facilitates earlier therapeutic interventions.
- This assay offers significant advantages over traditional culture methods for diagnosing invasive GAS pneumonia complicated by pleural effusion.
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.IMPORTANCEGroup 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%).
