Point-of-Care Air Surveillance of Respiratory Pathogens Using the GeneXpert® System
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Advances in air-based surveillance of pathogen genetic material are hindered by reliance on centralized, time-consuming molecular techniques. Point-of-care (POC) diagnostic platforms, like the Cepheid® GeneXpert®, offer rapid, simplified testing in clinical settings but have not been evaluated for use with air samples. Here, we paired the ThermoFisher™ AerosolSense™ air sampler with the Xpert® Xpress SARS-CoV-2/Flu/RSV Plus test to evaluate near-real-time air surveillance. To assess analytical sensitivity, we spiked collection substrates with inactivated viruses and performed overnight sampling using the air sampler. As few as 10 copies of influenza A/B (IAV/IBV) and RSV applied to the substrate were detectable by GeneXpert, while SARS-CoV-2 required at least 100 copies for detection. Longitudinal air surveillance was conducted across congregate settings in Columbia, Missouri, and Madison, Wisconsin, in 2024-2025, collecting 281 air samples. SARS-CoV-2 was detected most frequently, followed by IAV. To assess concordance, 191 samples with paired GeneXpert and RT-qPCR results were analyzed across multiple Ct value cutoffs. Agreement between GeneXpert and RT-qPCR for SARS-CoV-2 was fair to moderate (κ = 0.306–0.443). Optimal GeneXpert Ct cutoffs for the best balance between sensitivity and specificity, determined using analyses such as Youden’s index, were site-specific: 45 for Wisconsin (67% sensitivity, 83% specificity) and 41 for Missouri (76% sensitivity, 62% specificity), reflecting differences in laboratory protocols. For IAV, agreement was moderate (κ = 0.56) with GeneXpert Ct cutoff of 40, achieving 85% sensitivity and 81% specificity. Further studies across diverse settings and viral targets are needed to establish GeneXpert’s role in routine air surveillance.
Importance
This study demonstrates that point-of-care molecular testing with the Cepheid® GeneXpert® provides a faster alternative to the time-consuming molecular workflows currently used for detecting airborne respiratory pathogens. The GeneXpert provides results within 37 minutes after sample addition to the Xpress CoV-2/Flu/RSV test cartridge (following approximately 20 minutes for sample elution), compared to the multiple hours or days required by laboratory-based methods, enabling mitigation measures before widespread transmission occurs. Integrating GeneXpert testing with air sampling offers a simple, semi-automated approach for pathogen detection in healthcare and community settings. Because GeneXpert instruments are already deployed in over 180 countries, including clinics in low- and middle-income settings, this approach can extend air sampling–based surveillance to regions where individual patient testing is not feasible. These workflows can also be adapted to detect other pathogens with point-of-care assays.
