Here, we report on the FA-PP panel testing of LRT (BAL fluid or ETA) samples from ICU-admitted COVID-19 patients over a 5-month period (September 2020 to March 2021). The goal of this implementation was to avoid unnecessarily or inappropriately administered antimicrobials to prevent infectious complications in patients with COVID-19.
CID EPISODE 1135 PLUS
In September 2020, when the second wave of the SARS-CoV-2 pandemic was raging in Italy, we implemented the multiplexed, semiquantitative FilmArray pneumonia plus (FA-PP) panel (BioFire, Salt Lake City, UT, USA) assay ( 12, – 14) for routine clinical use at our institution (a large Italian university hospital). However, the impact of these assays on antibiotic use has scarcely been explored. In this context, newer multiplex PCR-based or array-based multipathogen and, conditionally, antimicrobial resistance (AMR) gene detection assays helped to diagnose bacterial infection (either secondary or concomitant to SARS-CoV-2 infection) in ICU patients with COVID-19 ( 1, 5, 10, 11). Whenever feasible ( 8), sampling of lower respiratory tract (LRT) secretions (i.e., obtaining bronchoalveolar lavage fluid or endotracheal aspirate samples) is crucial to provide detection of organisms coupled with assessment of their bacterial loads in COVID-19 patients who develop VAP or non-VAP hospital-acquired pneumonia (HAP) during the ICU stay ( 9). Since the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of human coronavirus disease 2019 (COVID-19), bacterial pneumonia, mostly ventilator-associated pneumonia (VAP), has been reported as a relatively frequent COVID-19 complication in critically ill patients, such as those admitted to the intensive care unit (ICU) ( 1, – 7). A better understanding of the role of that or similar PCR assays in routine ICU practice may lead us to appreciate the effectiveness of their implementation during the COVID-19 pandemic. We report on the actual implementation of rapid diagnostics and its real-life impact on patient treatment, which is a gain over previously published studies on the topic. We showed that a PCR-based, culture-independent laboratory assay allows not only accurate diagnosis but also streamlining of antimicrobial therapy for bacterial pneumonia episodes. IMPORTANCE Since bacterial pneumonia is relatively frequent, suspicion of it in COVID-19 patients may prompt ICU clinicians to overuse (broad-spectrum) antibiotics, particularly when empirical antibiotics do not cover the suspected pathogen. Compared to standard-of-care testing, the FA-PP panel may be of great value in the management of COVID-19 patients at risk of developing bacterial pneumonia in the ICU. Excluding 19 colistin-resistant Acinetobacter baumannii episodes, AST confirmed appropriate antibiotic receipt in 101 (84.2%) of 120 episodes for one or more FA-PP-detected organisms. Antimicrobial-resistant organisms caused 78 (60.0%) of 120 episodes. Overall, antibiotics were initiated in 87 (72.5%) of 120 pneumonia episodes and were not administered in 80 (87.0%) of 92 nonpneumonia episodes.
Antibiotics were discontinued in 5 (33.3%) of 15 patients with FA-PP-negative samples and were escalated/deescalated in 39 (88.6%) of 44 patients with FA-PP-positive samples. Fifty-nine (27.8%) of 212 samples were from empirically treated patients. FA-PP detected no culture-growing organisms (mostly Staphylococcus aureus or Pseudomonas aeruginosa) in 19 of 120 samples or antimicrobial resistance genes in two culture-negative samples for S. Etiologically, 120 samples were positive by both methods, two samples were culture positive but FA-PP negative (i.e., negative for on-panel organisms), and 90 were negative by both methods.
We tested 212 samples from 150 patients suspected of bacterial pneumonia. Changes to targeted and/or appropriate antimicrobial therapy were reviewed. Respiratory samples were collected from patients who were mechanically ventilated at the time bacterial etiology and antimicrobial resistance were determined using both standard-of-care (culture and antimicrobial susceptibility testing ) and FA-PP panel testing methods. Upon its implementation, the FilmArray pneumonia plus (FA-PP) panel’s practicability for both the diagnosis and antimicrobial therapy management of bacterial pneumonia was assessed in ICU patients with COVID-19. Bacterial pneumonia is a challenging coronavirus disease 2019 (COVID-19) complication for intensive care unit (ICU) clinicians.
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