Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates
Abstract 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 inve...
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2021-07-01
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Series: | Antimicrobial Resistance and Infection Control |
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Online Access: | https://doi.org/10.1186/s13756-021-00978-9 |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 |
spellingShingle |
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 Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates Antimicrobial Resistance and Infection Control Cepheid GeneXpert Real-time PCR Rapid diagnostics VAP Ventilator-associated pneumonia |
author_facet |
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 |
author_sort |
Thomas Ewout van der Schalk |
title |
Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates |
title_short |
Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates |
title_full |
Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates |
title_fullStr |
Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates |
title_full_unstemmed |
Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates |
title_sort |
evaluation of genexpert pa assay compared to genomic and (semi-)quantitative culture methods for direct detection of pseudomonas aeruginosa in endotracheal aspirates |
publisher |
BMC |
series |
Antimicrobial Resistance and Infection Control |
issn |
2047-2994 |
publishDate |
2021-07-01 |
description |
Abstract 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. |
topic |
Cepheid GeneXpert Real-time PCR Rapid diagnostics VAP Ventilator-associated pneumonia |
url |
https://doi.org/10.1186/s13756-021-00978-9 |
work_keys_str_mv |
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doaj-2c041679eeed4e209132e3d63a661cb12021-07-25T11:42:35ZengBMCAntimicrobial Resistance and Infection Control2047-29942021-07-0110111010.1186/s13756-021-00978-9Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspiratesThomas Ewout van der Schalk0Jasmine Coppens1Leen Timbermont2Agata Turlej-Rogacka3Liesbet Van Heirstraeten4Matilda Berkell5Li Yu6Christine Lammens7Basil Britto Xavier8Veerle Matheeussen9Margareta Ieven10Michael McCarthy11Philippe G. Jorens12Alexey Ruzin13Mark T. Esser14Samir Kumar-Singh15Herman Goossens16Surbhi Malhotra-Kumar17Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpStatistical Sciences, BioPharmaceuticals R&D, AstraZenecaLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpLaboratory of Clinical Microbiology, Antwerp University HospitalLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpEarly-Stage Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZenecaDepartment of Intensive Care Medicine , Antwerp University HospitalMicrobial Sciences, BioPharmaceuticals R&D, AstraZenecaMicrobial Sciences, BioPharmaceuticals R&D, AstraZenecaLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpLaboratory of Medical Microbiology, Vaccine and Infectious Disease Institute , University of AntwerpAbstract 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.https://doi.org/10.1186/s13756-021-00978-9CepheidGeneXpertReal-time PCRRapid diagnosticsVAPVentilator-associated pneumonia |