Respiratory bacterial co-infections in intensive care unit-hospitalized COVID-19 patients: Conventional culture vs BioFire FilmArray pneumonia Plus panel

• DOI: 10.1016/j.mimet.2021.106259
• Publication Date: 2021-05-29T23:59:18Z
• Authors: Claudio Foschi; Anna Zignoli; Paolo Gaibani; Caterina Vocale; Giada Rossini; Silvia Lafratta; Andrea Liberatore; Gabriele Turello; Tiziana Lazzarotto; Simone Ambretti
• Keywords: Adult; 0303 health sciences; FilmArray; Bacteria; SARS-CoV-2; Coinfection; Coinfections; Respiratory infections; COVID-19; Sensitivity and Specificity; Article; Bacterial Typing Techniques; 3. Good health; Intensive Care Units; 03 medical and health sciences; COVID-19; Coinfections; FilmArray; Respiratory infections; SARS-CoV-2; Humans; Multiplex Polymerase Chain Reaction; Respiratory Tract Infections; Retrospective Studies

The prevalence and microbiology of concomitant respiratory bacterial infections in patients with SARS-CoV-2 infection are not yet fully understood. In this retrospective study, we assessed respiratory bacterial co-infections in lower respiratory tract samples taken from intensive care unit-hospitalized COVID-19 patients, by comparing the conventional culture approach to an innovative molecular diagnostic technology. A total of 230 lower respiratory tract samples (i.e., bronchial aspirates or bronchoalveolar lavages) were taken from 178 critically ill COVID-19 patients. Each sample was processed by a semi-quantitative culture and by a multiplex PCR panel (FilmArray Pneumonia Plus panel), allowing rapid detection of a wide range of clinically relevant pathogens and a limited number of antimicrobial resistance markers. More than 30% of samples showed a positive bacterial culture, with Pseudomonas aeruginosa, Klebsiella pneumoniae and Staphylococcus aureus the most detected pathogens. FilmArray showed an overall sensitivity and specificity of 89.6% and 98.3%, respectively, with a negative predictive value of 99.7%. The molecular test significantly reduced the turn-around-time (TAT) and increased the rates of microbial detection. Most cases missed by culture were characterized by low bacterial loads (104-105 copies/mL). FilmArray missed a list of pathogens not included in the molecular panel, especially Stenotrophomonas maltophilia (8 cases). FilmArray can be useful to detect bacterial pathogens in lower respiratory tract specimens of COVID-19 patients, with a significant decrease of TAT. The test is particularly useful to rule out bacterial co-infections and avoid the inappropriate prescription of antibiotics.