Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates

Thomas Ewout van der Schalk, Jasmine Coppens, Leen Timbermont, Agata Turlej-Rogacka, Liesbet Van Heirstraeten, Matilda Berkell, Li Yu, Christine Lammens, Basil Britto Xavier, Veerle Matheeussen, Margareta Ieven, Michael McCarthy, Philippe G Jorens, Alexey Ruzin, Mark T Esser, Samir Kumar-Singh, Herman Goossens, Surbhi Malhotra-Kumar

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INTRODUCTION: Pseudomonas aeruginosa is a common cause of ventilator-associated pneumonia (VAP). Rapid and accurate detection of lower respiratory tract colonization and/or infection with P. aeruginosa may advise targeted preventive (antibody-based) strategies and antibiotic therapy. To investigate this, we compared semi-quantitative culture results from 80 endotracheal aspirates (ETA) collected from mechanically-ventilated patients, to two culture and two non-culture-based methods for detection of P. aeruginosa.

METHODS: P. aeruginosa-positive (n = 40) and -negative (n = 40) ETAs from mechanically ventilated patients analyzed initally by (i) routine semi-quantitative culture, were further analyzed with (ii) quantitative culture on chromogenic ChromID P. aeruginosa and blood agar; (iii) enrichment in brain heart infusion broth followed by plating on blood agar and ChromID P. aeruginosa; (iv) O-antigen acetylase gene-based TaqMan qPCR; and (v) GeneXpert PA PCR assay.

RESULTS: Of the 80 ETA samples included, one sample that was negative for P. aeruginosa by semi-quantitative culture was found to be positive by the other four methods, and was included in an "extended" gold standard panel. Based on this extended gold standard, both semi-quantitative culture and the GeneXpert PA assay showed 97.6% sensitivity and 100% specificity. The quantitative culture, enrichment culture and O-antigen acetylase gene-based TaqMan qPCR had a sensitivity of 97.6%, 89.5%, 92.7%, and a specificity of 97.4%, 100%, and 71.1%, respectively.

CONCLUSION: This first evaluation of the GeneXpert PA assay with ETA samples found it to be as sensitive and specific as the routine, hospital-based semi-quantitative culture method. Additionally, the GeneXpert PA assay is easy to perform (hands-on time ≈ 5 min) and rapid (≈ 55 min assay time). The combination of the high sensitivity and high specificity together with the rapid acquisition of results makes the GeneXpert PA assay a highly recommended screening technique. Where this equipment is not available, semi-quantitative culture remains the most sensitive of the culture methods evaluated here for P. aeruginosa detection in ETA samples.

Original languageEnglish
Article number110
JournalAntimicrobial Resistance and Infection Control
Issue number1
Publication statusPublished - 2021


  • Bacteriological Techniques/methods
  • Belgium
  • Genomics
  • Humans
  • Polymerase Chain Reaction
  • Pseudomonas aeruginosa/isolation & purification
  • Respiration, Artificial
  • Sensitivity and Specificity
  • Trachea/microbiology


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