Diagnostic Concordance Between Multiplex PCR 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.

Abstract BackgroundDetection of co-infections is important to initiate appropriate antimicrobial therapy. Molecular diagnostic testing identifies pathogens at a greater rate than conventional microbiology. We assessed both bacterial co-infections identified in culture or multiplex PCR FilmArray® Pneumonia Panel (FA-PNEU) in patients infected with SARS-CoV-2 in ICU and the concordance between these techniques.MethodsProspective study of patients with SARS-CoV-2 who were hospitalized for no more than 48 hours, in mechanical ventilation no longer than 24 hours in 8 ICUs in Medellín, Colombia. We studied mini-bronchoalveolar lavage or endotracheal aspirate samples processed in conventional culture and FA-PNEU. Co-infection was defined as the identification of a respiratory pathogen using FA-PNEU or cultures.ResultsOf 110 patients who underwent both methods, FA-PNEU and culture-positive samples comprised 24.54% vs 17.27%, respectively. 18 samples were positive for both techniques, 82 were negative, one was culture-positive with negative FA-PNEU, and 9 were FA-PNEU-positive with negative culture. The two bacteria most frequently detected by FA-PNEU were Staphylococcus aureus (37.5%) and Streptococcus agalactiae (20%) and by culture were Staphylococcus aureus (34.78%) and Klebsiella pneumoniae (26.08%). The overall concordance was 90.1% and by microorganism it was between 92.7% and 100%. Positive predictive values (PPV) were between 50% and 100%, being lower for Enterobacter cloacae and Staphylococcus aureus. Negative predictive values (NPV) were high (between 99.1% and 100%); MecA/C/MREJ had a specificity of 94.55% and a NPV of 100%.ConclusionsThe overall concordance was 90.1%, and it was between 92.7% and 100% by microorganisms. The positive qualitative agreement was between 50% and 100%, with a very high NPV.