Evaluation of the BioFire FilmArray Pneumonia Panel for Detection of Viral and Bacterial Pathogens in Lower Respiratory Tract Specimens in the Setting of a Tertiary Care Academic Medical Center

Abstract

Our objective was to evaluate the diagnostic yield and accuracy of the BioFire FilmArray pneumonia panel (BFPP) for identification of pathogens in lower respiratory tract specimens (n = 200) from emergency department (ED) and intensive care unit (ICU) patients at a tertiary care academic medical center. Specimens were collected between January and November 2018, from patients ≥18 years of age, and culture was performed as part of standard-of-care testing. The BFPP identified a viral or bacterial target in 117/200 (58.5%) samples, including Staphylococcus aureus in 22% of samples and Haemophilus influenzae in 14%, and both a viral and bacterial target in 4% of samples. The most common viruses detected by BFPP were rhinovirus/enterovirus (4.5%), influenza A virus (3%), and respiratory syncytial virus (RSV) (2%). Overall, there was strong correlation between BFPP and standard methods for detection of viruses (99.2%) and bacteria (96.8%). Most bacteria (60/61 [98.4%]) detected by standard methods were also identified by BFPP, and 92 additional bacteria were identified by BFPP alone, including 22/92 (23.9%) additional S. aureus isolates and 25/92 (27.2%) H. influenzae isolates, which were more frequently discordant when detected at low concentrations (S. aureus, P < 0.001; H. influenzae, P < 0.0001) and in sputum-type specimens (S. aureus, P < 0.05). A potential limitation of the BFPP assay is the absence of fungal targets and Stenotrophomonas maltophilia, which were detected in 26 and 4 of 200 specimens, respectively. Real-time specimen analysis with BFPP has the potential to identify bacterial pathogens and resistance markers 44.2 and 56.3 h faster than culture-based methods. The BFPP is a rapid and accurate method for detection of pathogens from lower respiratory tract infections.

Keywords: BioFire; pneumonia; quantitative PCR; syndromic testing.

FIG 1

Study design. A total of 200 consecutively available lower respiratory tract samples were collected between January and November 2018. Samples were from adult patients with respiratory symptoms at a large tertiary care academic medical center. Remnant samples were stored at –80°C prior to being tested with the BFPP on the BioFire FilmArray 2.0. Antibiotic utilization and standard-of-care test results were obtained by retrospective chart review, and these data were used to determine turnaround time and test performance characteristics.

FIG 2

BFPP detection. Panel a shows that BFPP detected a bacterium or virus in 117/200 (58.5%) of samples, with similar distributions between sample types (P = 0.36 [chi-square test] and degrees of freedom [df] = 3). Panel b demonstrates that more than one pathogen was detected by BFPP in 50/116 (43%) of positive samples.

FIG 3

Concordance of BFPP with standard of care (SOC) for viral and bacterial identification. Panel a shows a high overall agreement (99%) of BFPP with SOC for detection of viruses. Panel b shows a predominance of S. aureus and H. influenzae among detected bacterial targets and displays 92 bacterial targets detected by BFPP and not by SOC testing.

FIG 4

Discordant detection of S. aureus and H. influenzae by bacterial quantity (left) and specimen type (right). Multivariate, least-squares, linear regression demonstrates that S. aureus (a and b) and H. influenzae (c and d) quantity as measured by BFPP was directly and independently associated with concordant detection by BFPP and SOC culture, compared to detection by BFPP alone (S. aureus model, r-squared = 0.35 and df = 37; H. influenzae model, r-squared = 0.57 and df = 21). P values from regression coefficients are represented as follows: ***, P < 0.001; **, P < 0.01; *, P < 0.05; and ns, nonsignificant. Values inside columns represent the number of samples per horizontal-axis category as grouped by test concordance.

FIG 5

Projected time savings with BFPP compared to SOC aerobic culture. Turnaround time for the BioFire upper respiratory panel (surrogate for BFPP) was significantly shorter (****, P < 0.0001) than SOC culture for identification (ID) of bacteria (42.2-h reduction). Likewise, the turnaround time for detection of antimicrobial resistance (AMR) markers by BFPP was shorter (P < 0.0001) than determination of antimicrobial susceptibility by standard phenotypic methods (56.3-h reduction). Comparisons were made via two-tail, unpaired t tests.

FIG 6

Length of hospital stay and 30-day mortality grouped by test concordance between BFPP and SOC aerobic culture for detection of S. aureus and H. influenzae. One-way analysis of variance (ANOVA) demonstrates that length of hospital stay (left) was not significantly different for S. aureus [F(2,195) = 0.088, P = 0.92] (a) or H. influenzae [F(2,195) = 0.135, P = 0.87] (c) detected by both BFPP and SOC culture compared to detection by BFPP alone. Two-sided Fisher’s exact test demonstrated that 30-day mortality (right) was not significantly different for S. aureus (P = 0.74) (b) or H. influenzae (P = 0.15) (d) detected by both BFPP and SOC compared detection by BFPP alone. Values inside columns represent the number of patient deaths per x axis group that occurred within 30 days following aerobic culture testing.