Diagnostic concordance between BioFire® FilmArray® Pneumonia Panel and culture in patients with COVID-19 pneumonia admitted to intensive care units: the experience of the third wave in eight hospitals in Colombia

• Published in: Critical care (London, England) England), 2022-05, Vol.26 (1), p.130-130, Article 130
• Main Authors: Molina, Francisco José, Botero, Luz Elena, Isaza, Juan Pablo, Cano, Luz Elena, López, Lucelly, Tamayo, Leidy, Torres, Antoni
• Format: Article
• Language: English
• Subjects: Anti-Bacterial Agents - therapeutic use; Antibiotics; Bacteria; Bacterial coinfection; Bacterial pneumonia; Coinfection; Colombia; Comorbidity; Complications and side effects; Confidence intervals; Coronaviruses; COVID-19; COVID-19 - diagnosis; Critical care; Deoxyribonucleic acid; Diagnosis; DNA; FilmArray; Health aspects; Hospitalization; Hospitals; Humans; Infections; Intensive care; Intensive Care Units; Intubation; Laboratories; Medical diagnosis; Microorganisms; Mortality; Multiplex Polymerase Chain Reaction - methods; Pathogenic microorganisms; Pathogens; Patient outcomes; Pneumonia; Pneumonia - drug therapy; Prospective Studies; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Statistics; Ventilators
• ISSN: 1364-8535; 1466-609X; 1364-8535; 1366-609X
• DOI: 10.1186/s13054-022-04006-z

The detection of coinfections is important to initiate appropriate antimicrobial therapy. Molecular diagnostic testing identifies pathogens at a greater rate than conventional microbiology. We assessed both bacterial coinfections identified via culture or the BioFire® FilmArray® Pneumonia Panel (FA-PNEU) in patients infected with SARS-CoV-2 in the ICU and the concordance between these techniques. This was a prospective study of patients with SARS-CoV-2 who were hospitalized for no more than 48 h and on mechanical ventilation for no longer than 24 h in 8 ICUs in Medellín, Colombia. We studied mini-bronchoalveolar lavage or endotracheal aspirate samples processed via conventional culture and the FA-PNEU. Coinfection was defined as the identification of a respiratory pathogen using the FA-PNEU or cultures. Serum samples of leukocytes, C-reactive protein, and procalcitonin were taken on the first day of intubation. We analyzed the empirical antibiotics and the changes in antibiotic management according to the results of the FA-PNEUM and cultures. Of 110 patients whose samples underwent both methods, FA-PNEU- and culture-positive samples comprised 24.54% versus 17.27%, respectively. Eighteen samples were positive in both techniques, 82 were negative, 1 was culture-positive with a negative FA-PNEU result, and 9 were FA-PNEU-positive with negative culture. The two bacteria most frequently detected by the FA-PNEU were Staphylococcus aureus (37.5%) and Streptococcus agalactiae (20%), and those detected by culture were Staphylococcus aureus (34.78%) and Klebsiella pneumoniae (26.08%). The overall concordance was 90.1%, and when stratified by microorganism, it was between 92.7 and 100%. The positive predictive value (PPV) was between 50 and 100% and were lower for Enterobacter cloacae and Staphylococcus aureus. The negative predictive value (NPV) was high (between 99.1 and 100%); MecA/C/MREJ had a specificity of 94.55% and an NPV of 100%. The inflammatory response tests showed no significant differences between patients whose samples were positive and negative for both techniques. Sixty-one patients (55.45%) received at least one dose of empirical antibiotics. The overall concordance was 90.1%, and it was between 92.7% and 100% when stratified by microorganisms. The positive predictive value was between 50 and 100%, with a very high NPV.