Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens

Evaluation of the FilmArray® Pneumonia Plus Panel for Rapid Diagnosis of Hospital-Acquired Pneumonia in Intensive Care Unit Patients

“…However, it should be noted that the overall prevalence of antimicrobial resistance was low in our study, and it should also be kept in mind that a lack of detection of resistance genes does not necessarily means susceptibility to antibiotics as there are resistance mechanisms that are not detected by FAPP (i.e., derepressed or plasmidic cephalosporinases, or non-CTX-M ESBL). Regarding methicillin resistance, consistent with previous observations, we noticed the false-positive detection of mecA/C and MREJ genes in one specimen containing a MSSA in culture (Yoo et al, 2020). Since this respiratory sample was polymicrobial, we hypothesized that it could have contained both a methicillin-resistant coagulase-negative Staphylococcus carrying mecA/C, and a MSSA with an empty SCCmec cassette (thus positive for MRJE) (Murphy et al, 2020).…”

“…Thus, the multiplex panel identified mixed infections in 49/100 patients (58.1% of positive BAL DS or ETA DS ), compared to 32/100 patients (51.9% and 34.6% of positive BAL DS and ETA DS , respectively) by culture. These data corroborate other published results, and outline that the true incidence of polymicrobial HAP is probably underestimated with conventional techniques (Lee et al, 2019;Buchan et al, 2020;Murphy et al, 2020;Yoo et al, 2020). It remains to be evaluated whether detection of more pathogens will increase cure rates, and not adversely result in unnecessary consumption of broad-spectrum antimicrobials.…”

“…The most common pathogen of our study, H. influenzae, was detected with FAPP in 40/100 patients at diagnosis, after a median length of ICU stay of 4 days, but was less frequently found in culture (29/100 patients). In line with our data, the majority of discrepancies previously reported between FAPP and culture, concerned the same fastidious bacteria, and were explained by the higher sensitivity of the molecular test and/or antibiotics consumption before sampling (Lee et al, 2019;Yoo et al, 2020). Here, in just over half of the discrepant cases, H. influenzae grew on the enriched medium used for culture, but was overgrown by other pathogens or commensal bacteria, and was therefore not detected and/or not reported.…”

“…As expected, implementation of FAPP shortened the delay in getting results (4 h 15 min on average, one ICU setting being located 10 km away from the laboratory vs. 64-70 h with culture). In accordance with recent evaluations (Lee et al, 2019;Buchan et al, 2020;Murphy et al, 2020;Yoo et al, 2020), FAPP increased the positivity rate of diagnostic testing (81.6% for BAL DS , and 75.6% for ETA DS ), enabling identification of additional bacteria in 39.5% BAL DS and 37.8% ETA DS . The most common pathogens detected were consistently the same across both methods (i.e., in order of prevalence, H. influenzae, S. aureus, E. coli, S. pneumoniae, and K. pneumoniae).…”

Performance of a multiplex polymerase chain reaction panel for identifying bacterial pathogens causing pneumonia in critically ill patients with COVID-19

“…Molecular tests provide a rapid turnaround time (TAT), together with identifications and semi-quantitative results for many pathogens responsive to antimicrobial therapy. Multiplex testing may provide additional information concerning the presence of antibiotic resistance genes, thereby improving antibiotic management ( Lee et al, 2019 ; Yoo et al, 2020 ). We performed a prospective single-center study on critically ill patients with COVID-19, in which we conducted parallel tests of blind bronchoalveolar lavage (BBAL) by conventional culture and FilmArray® Pneumonia Plus (FA-PP) panel (BioFire, Salt Lake City, US).…”