Performance of a Semiquantitative Multiplex Bacterial and Viral PCR Panel Compared With Standard Microbiological Laboratory Results: 396 Patients Studied With the BioFire Pneumonia Panel

Abstract

Background Microbiologic results are critical to optimal management of patients with lower respiratory tract infection, but standard methods may take several days. The multiplex PCR BioFire® Pneumonia (PN) panel detects 15 common bacterial species semi-quantitatively as copy number/mL, 8 viral species and 7 resistance genes in about an hour within the clinical laboratory. Methods We tested 396 unique endotracheal or bronchoalveolar lavage specimens with the BioFire® Pneumonia panel, and compared the bacterial detections to conventional gram stain and culture results. Results Of the 396 patients, 180 grew at least 1 bacteria that had a target on the PN panel and 177/180 (98.3%) were detected by the panel. A further 20% of patients had additional targets detected, but not found in standard culture (specificity 69%, positive predictive value 63%, and negative predictive value 98.9%). Copy number was strongly related to standard semi-quantitative growth on plates reported by the laboratory (e.g. 1+, 2+, 3+ growth), and was significantly higher in those specimens that grew a potential pathogen. Both higher copy number and bacterial detections found by the PN panel, but not found in culture, were strongly positively related to the level of WBC reported in the initial gram stain. Conclusions Higher copy number and bacterial detections per se by the PN panel are related to the host respiratory tract inflammatory response. If laboratories can achieve a rapid turnaround time, the PN panel should have a significant impact both to patient management and to antibiotic stewardship.

Identification of bacterial co-detections in COVID-19 critically Ill patients by BioFire® FilmArray® pneumonia panel: a systematic review and meta-analysis

“…The variation based on culture reporting process is further suggested by our data as the heterogeneity among BioFire PN plus detections was much lower than culture (I 2 32% vs 93%). In another study, the clinical relevance of increased detections was recently explored, reflecting strong positive correlations to level of WBC on gram stain thus indicating a correlation of inflammation with these detections [Rand et al, 2020] . Finally, the increased sensitivity over culture has been demonstrated in a European multicenter study of the BioFire PN plus , the Curetis® Unyvero® Pneumonia Panel, and 16S metagenomic analysis which reflected consistency in detections among molecular platforms as being more sensitive than culture [Virve I Enne1 et al, 2020] .…”

Clinical decision making is improved by BioFire Pneumonia Plus in suspected lower respiratory tract infection after lung transplantation: Results of the prospective DBATE‐IT* study

“…The utility of the BFPPp and the previous generation BFPP, featuring a similar panel except for the absence of MERS-CoV, were studied in intensive care unit and other in-patient settings and demonstrated a shortened response time and equal or even better sensitivity compared to conventional diagnostics. [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] In LTx patients, PCR-based testing from BAL has previously been described in the context of viral infections, impossible-to-cultivate atypical bacteria, and Pneumocystis jirovecii. 12,13,38,39 Recent studies have evaluated PCR-based testing for specific fungal pathogens and Nocardia.…”

“…While we aimed to provide real-life data on the use of BFPPp in LRTI In conclusion, our findings match those of other groups evaluating the use of BFPPp in settings other than LRTI in LTx recipients. [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] The BFPPp significantly decreased the response time in the treatment of LRTI in an outpatient setting, with same-day results available in all but two cases. While BFPPp was a useful tool in the diag-…”

“…17 Recent studies demonstrate that BFPPp and the earlier BioFire Pneumonia panel (BFPP) perform well in both sputum and BAL samples in a variety of settings outside the context of LTx. [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] Furthermore, the older BFPP was recently shown to allow for faster clinical decisions while retaining good overall concordance with conventional diagnostics in LTx recipients. 31 Notably, the majority of patients in this study underwent bronchoscopy for routine surveillance, not due to suspected LRTI.…”

Pseudomonas aeruginosa in Bronchiectasis

“…Studies report high overall percentage agreement between the pneumonia panel, SOC cultures, and Gram staining. [56][57][58][59] However, concordance was lower for specimens at thresholds less than 10 6 CFU/mL and higher (90.9-100%) for specimens 10 6 CFU/mL. 58 Further work is needed to determine if organisms detected at low abundances in molecular tests, but not in SOC cultures, are significant for patient outcomes.…”