Comparison of GeneXpert MRSA/SA ETA assay with semi-quantitative and quantitative cultures and nuc gene-based qPCR for detection of Staphylococcus aureus in endotracheal aspirate samples

Jasmine Coppens, Liesbet Van Heirstraeten, Alexey Ruzin, Li Yu, Leen Timbermont, Christine Lammens, Veerle Matheeussen, Michael McCarthy, Philippe Jorens, Margareta Leven, Samir Kumar-Singh, Herman Goossens, Surbhi Malhotra-Kumar

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Introduction: Staphylococcus aureus (S. aureus) is a common cause of ventilator-associated pneumonia. Rapid and accurate detection of lower respiratory tract colonization and/or infection with S. aureus may inform targeted preventive and therapeutic strategies. To investigate this, we compared semi-quantitative (SQ)-culture results from 79 endotracheal aspirates (ETA) collected from mechanically-ventilated patients, to two culture and two non-culture-based methods for detection of S. aureus.

Methods: ETA analyzed by routine SQ-culture on blood and colistin-nalidixic-acid agar was compared to: (i) quantitative (Q-) culture on chromogenic COLOREX™ Staph aureus; (ii) enrichment in brain-heart-infusion broth followed by plating on blood agar and COLOREX™; (iii) nuc-based TaqMan qPCR, and (iv) GeneXpert MRSA/SA ETA assay.

Results: Of the 79 ETA samples analyzed by SQ-culture, 39 samples were positive, and 40 negative for S. aureus. Two samples negative for S. aureus by SQ-culture were, however, S. aureus-positive by the other four methods and were considered positive. Appending these two samples as positive in the SQ-culture results, sensitivities-specificities for Q-culture, enrichment-culture, TaqMan qPCR and GeneXpert were 100-95, 100-92, 100-53% and 100% - 100, respectively. The lower specificities of Q-culture, enrichment-culture, and TaqMan qPCR was because of their higher sensitivities, although TaqMan qPCR also detected S. aureus-specific extracellular DNA.

Conclusion: This first evaluation of the GeneXpert MRSA/SA ETA assay with ETA samples found it to be highly sensitive, specific, user-friendly (hands-on time ~ 5 min.), and rapid (~ 66 min. assay time). Where this equipment is not available, we recommend implementing more sensitive culture-based methods for improved S. aureus detection in ETA samples.

Original languageEnglish
Article number4
JournalAntimicrobial Resistance and Infection Control
Publication statusPublished - 2019


  • Bacterial Proteins/genetics
  • Diagnostic Tests, Routine/methods
  • Humans
  • Methicillin-Resistant Staphylococcus aureus/classification
  • Micrococcal Nuclease/genetics
  • Pneumonia, Ventilator-Associated
  • Real-Time Polymerase Chain Reaction
  • Sensitivity and Specificity
  • Staphylococcal Infections/diagnosis
  • Staphylococcus aureus/classification
  • Ventilators, Mechanical/microbiology

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