Diagnosis and Treatment of Bacterial Pneumonia in Critically Ill Patients with COVID-19 Using a Multiplex PCR Assay: A Large Italian Hospital’s Five-Month Experience

Abstract

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. 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.

The Biofire® Filmarray® Pneumonia Plus panel for management of lower respiratory tract infection in mechanically-ventilated patients in the COVID-19 era: a diagnostic and cost-benefit evaluation

“…This figure varies widely across the aforementioned studies, likely reflecting differences in bacterial targets present in the specimens and EAT usage at time of testing [16] . Similarly, in line with previously published data [ 8 , 13 , [15] , [16] , [17] , 21 ], use of FA-PP increased the detection of antimicrobial-resistant bacteria.…”

“…This provides further proof that FA-PP increases the bacterial detection yield compared with standard culture. These figures were higher than those previously published by Buchan et al ., (94.8% and 63.3%) [16] , and Lee et al ., (a 70.3% increase in total bacterial targets detected by the PN panel) [21] , probably due to the extensive use of EAT among patients in the current study. In our experience, the PPA between qualitative results returned by FA-PP and standard culture was 44% overall, and higher for Enterobacterales compared with NF-GNB, other GNB and GPC.…”

“…A large number of studies have evaluated the diagnostic performance of FA-PP compared to standard culture in patients with suspected LRTBI [7] , [8] , [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] ; nonetheless, cross-study comparison is not straightforward due to differences in potentially impactful parameters, such as patient's baseline clinical condition, hospitalization ward (ICU vs. non-ICU), LRTBI features (i.e., associated or not with MV), timing of FA-PP testing after hospital admission, specimens used (endotracheal aspirates vs. bronchoscopic specimens), and most importantly, whether or not EAT was in place at the time of testing. Despite these dissimilarities, all studies consistently showed the superior sensitivity of FA-PP for detection of all on-panel bacterial targets [7] , [8] , [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] . In line with this, we found that, compared with culture, FA-PP increased the number of specimens reported as positive by approximately 70% and the total number of bacterial targets detected by around 120%, irrespective of their nature.…”

“…Standard semiquantitative culture-based and antimicrobial susceptibility testing procedures performed on endotracheal aspirates or bronchoscopic specimens are lengthy, returning results approximately 48–72 h after specimen reception. The use of molecular diagnostic approaches that allow rapid bacterial identification and documentation of the presence of genotypic resistance traits in the causative bacteria may provide clinically actionable results within 2 h. One such approach is the BioFire® FilmArray® Pneumonia/Pneumonia plus Panel (FA-PP) (BioFire Diagnostics, LLC, Salt Lake City, UT), a multiplex PCR panel that allows detection of 15 bacteria commonly involved in VA-LRTBI, providing semiquantitative estimates of bacterial load and seven genetic markers of antibiotic resistance (mecA/C and MREJ, blaCTX-M,blaKPC, blaVIM, blaOXA-48-like, blaIMP, blaNDM) This test has been extensively evaluated and proven to increase the diagnostic yield in LRTBI compared with standard culture-based methods [6] , [7] , [8] , [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] . FA-PP shows great promise in improving the therapeutic management of VA-LRTBI, however, its positioning in laboratory diagnostic algorithms remains to be defined [22] .…”

Empiric Treatment in HAP/VAP: “Don’t You Want to Take a Leap of Faith?”

“…During the COVID-19 pandemic, Maataaoui et al revealed in a prospective cohort of 112 episodes (104 HAP-VAP) an early empirical therapeutic change in 34% of HAP-VAP episodes (of which 46.3% were withdrawn) when this panel was performed [106]. Another recent prospective study showed among COVID-19 ICU patients that antibiotics were initiated in 87 (72.5%) of 120 pneumonia episodes and were not administered in 80 (87.0%) of 92 non-pneumonia episodes based on FA results [107].…”