Nabil Gastli1, Julien Loubinoux1, Matthieu Daragon2, Jean-Philippe Lavigne3, Pierre Saint-Sardos4, Hélène Pailhoriès5, Carole Lemarié5, Hanaa Benmansour6, Camille d'Humières7, Lauranne Broutin8, Olivier Dauwalder9, Michael Levy10, Gabriel Auger11, Solen Kernéis12, Vincent Cattoir13. 1. Service de Bactériologie, Hôpital Cochin, AP-HP Centre, Université de Paris, Paris, France. 2. Laboratoire de bactériologie, CHU de Dijon, Dijon, France. 3. Service de Microbiologie, CHU Nîmes, Unité Inserm U1047, Université de Montpellier, Nîmes, France. 4. Laboratoire de Bactériologie, CHU de Clermont-Ferrand, Unité Inserm U1071, INRA USC2018, Université Clermont Auvergne, Clermont-Ferrand, France. 5. Laboratoire de bactériologie, CHU Angers, UPRES EA3859, SFR 4208, Université d'Angers, Angers, France. 6. Laboratoire de Microbiologie, Hôpital Lariboisière, AP-HP, UMR Inserm 1137 IAME, Université de Paris, France. 7. Laboratoire de Bactériologie, Hôpital Bichat, AP-HP, UMR Inserm 1137 IAME, Université de Paris, France. 8. Département des Agents Infectieux, CHU La Milétrie, Poitiers, France. 9. Institut des Agents Infectieux, Centre de Biologie et Pathologie Nord, Hospices Civils de Lyon, Unité Inserm U1111 CIRI, Lyon, France. 10. Service de Réanimation Pédiatrique, Hôpital Robert-Debré, AP-HP, Université Paris Diderot Sorbonne Paris Cité, Paris, France. 11. Service de Bactériologie-Hygiène hospitalière, CHU de Rennes, CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques), Rennes, France. 12. Equipe Mobile d'Infectiologie, Hôpital Cochin, AP-HP Centre, Université de Paris, Paris, France. 13. Service de Bactériologie-Hygiène hospitalière, CHU de Rennes, CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques), Rennes, France; Unité Inserm U1230, Université de Rennes 1, Rennes, France. Electronic address: vincent.cattoir@chu-rennes.fr.
Abstract
OBJECTIVES: To evaluate performances of the rapid multiplex PCR assay BioFire FilmArray Pneumonia Panel (FA-PP) for detection of bacterial pathogens and antibiotic resistance genes in sputum, endotracheal aspirate (ETA) and bronchoalveolar lavage (BAL) specimens. METHODS: This prospective observational study was conducted in 11 French university hospitals (July to December 2018) and assessed performance of FA-PP by comparison with routine conventional methods. RESULTS: A total of 515 respiratory specimens were studied, including 58 sputa, 217 ETA and 240 BAL. The FA-PP detected at least one pathogen in 384 specimens, yielding an overall positivity rate of 74.6% (384/515). Of them, 353 (68.5%) specimens were positive for typical bacteria while eight atypical bacteria and 42 resistance genes were found. While identifying most bacterial pathogens isolated by culture (374/396, 94.4%), the FA-PP detected 294 additional species in 37.7% (194/515) of specimens. The FA-PP demonstrated positive percentage agreement and negative percentage agreement values of 94.4% (95% CI 91.7%-96.5%) and 96.0% (95% CI 95.5%-96.4%), respectively, when compared with culture. Of FA-PP false-negative results, 67.6% (46/68) corresponded to bacterial species not included in the panel. At the same semi-quantification level (in DNA copies/mL for FA-PP versus in CFU/mL for culture), the concordance rate was 43.4% (142/327) for culture-positive specimens with FA-PP reporting higher semi-quantification of ≥1 log10 in 48.6% (159/327) of cases. Interestingly, 90.1% of detected bacteria with ≥106 DNA copies/mL grew significantly in culture. CONCLUSIONS: FA-PP is a simple and rapid molecular test that could complement routine conventional methods for improvement of diagnosis accuracy of pneumonia.
OBJECTIVES: To evaluate performances of the rapid multiplex PCR assay BioFire FilmArray Pneumonia Panel (FA-PP) for detection of bacterial pathogens and antibiotic resistance genes in sputum, endotracheal aspirate (ETA) and bronchoalveolar lavage (BAL) specimens. METHODS: This prospective observational study was conducted in 11 French university hospitals (July to December 2018) and assessed performance of FA-PP by comparison with routine conventional methods. RESULTS: A total of 515 respiratory specimens were studied, including 58 sputa, 217 ETA and 240 BAL. The FA-PP detected at least one pathogen in 384 specimens, yielding an overall positivity rate of 74.6% (384/515). Of them, 353 (68.5%) specimens were positive for typical bacteria while eight atypical bacteria and 42 resistance genes were found. While identifying most bacterial pathogens isolated by culture (374/396, 94.4%), the FA-PP detected 294 additional species in 37.7% (194/515) of specimens. The FA-PP demonstrated positive percentage agreement and negative percentage agreement values of 94.4% (95% CI 91.7%-96.5%) and 96.0% (95% CI 95.5%-96.4%), respectively, when compared with culture. Of FA-PP false-negative results, 67.6% (46/68) corresponded to bacterial species not included in the panel. At the same semi-quantification level (in DNA copies/mL for FA-PP versus in CFU/mL for culture), the concordance rate was 43.4% (142/327) for culture-positive specimens with FA-PP reporting higher semi-quantification of ≥1 log10 in 48.6% (159/327) of cases. Interestingly, 90.1% of detected bacteria with ≥106 DNA copies/mL grew significantly in culture. CONCLUSIONS: FA-PP is a simple and rapid molecular test that could complement routine conventional methods for improvement of diagnosis accuracy of pneumonia.
Authors: D Markussen; M Ebbesen; S Serigstad; H M S Grewal; Ø Kommedal; L Heggelund; C H van Werkhoven; D Faurholt-Jepsen; T W Clark; C Ritz; E Ulvestad; R Bjørneklett; S T Knoop Journal: Sci Rep Date: 2022-01-10 Impact factor: 4.379