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.

Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 9801902 Publication Model: Electronic Cited Medium: Internet ISSN: 1466-609X (Electronic) Linking ISSN: 13648535 NLM ISO Abbreviation: Crit Care Subsets: MEDLINE

Publication: London, UK : BioMed Central Ltd
Original Publication: London : Current Science Ltd, c1997-

COVID-19*/diagnosis ; Coinfection* ; Pneumonia*/drug therapy; Anti-Bacterial Agents/therapeutic use ; Bacteria ; Colombia ; Hospitals ; Humans ; Intensive Care Units ; Multiplex Polymerase Chain Reaction/methods ; Prospective Studies ; SARS-CoV-2

Background: 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.
Methods: 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.
Results: 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.
Conclusions: 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.
(© 2022. The Author(s).)

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Keywords: Bacterial coinfection; Bacterial pneumonia; COVID-19; FilmArray; Intensive care units

0 (Anti-Bacterial Agents)

Date Created: 20220509 Date Completed: 20220511 Latest Revision: 20220716

20240105

PMC9084542

10.1186/s13054-022-04006-z

35534867