Multiplex PCR Panel Evaluated for Diagnosis of Pneumonia

Population based studies in the USA estimate the incidence of community-acquired pneumonia at 250 cases per 100,000 residents/year. At any given time, 1% of hospitalized patients receive treatment for hospital-acquired pneumonia, rendering pneumonia the most common healthcare-associated infection.

Despite potential benefits of achieving a microbiological diagnosis of pneumonia, including identifying resistant pathogens and decreasing antimicrobial utilization, a number of factors limit the value of traditional diagnostics in clinical practice. Guidelines emphasize the need for rapid, cost-effective and accurate diagnostic tests for pneumonia.


Infectious Disease Specialists at the New York University Grossman School of Medicine (New York, NY, USA) prospectively examined sputum specimens submitted to the microbiology laboratory for bacterial culture. From 5/2019 to 1/2020, the list of submitted specimens was reviewed twice daily. Expectorated, induced and tracheal aspirate specimens were considered for inclusion. The pneumonia panel was performed on high-quality sputum specimens and the results were prospectively compared with sputum cultures and other tests performed per standard of care.

The BioFire FilmArray Pneumonia Panel (BioFire Diagnostics, Salt Lake City, UT, USA) was run within 24 hours of patient selection. A cutoff of ≥10⁵ copies/mL was applied for semiquantitative bacterial assays. The panel detects semi-quantitatively 15 bacterial agents to assist with differentiation between colonization and true infection, and qualitatively three atypical bacterial and eight viral agents. Antimicrobial resistance genes including the methicillin resistance genes mecA/C and MREJ, the carbapenemases KPC, NDM, Oxa-48-like, VIM, IMP and the extended spectrum Beta-lactamase CTX-M are also detected.

The scientists reported that 70 patients were included, 69 of whom completed a 5-day antimicrobial course for pneumonia and 14.3% died during hospitalization. There was a trend of higher rate of microbiologic diagnosis among the patients with culture submitted before antimicrobial administration (9/15 versus 20/55). The panel increased the microbiologic diagnosis from 29/70 to 59/70 patients. The per isolate analysis revealed an increase in the isolation of Haemophilus influenzae and Streptococcus pneumoniae. On review of empiric antimicrobials, there was potential for antimicrobial optimization in 56/70 patients, including nine bacteria among nine patients, not covered by empiric treatment and another 70 antimicrobials in 49 patients that could have been stopped.

The authors observed a significant increase in the rate of microbiologic diagnosis among adult patients hospitalized with pneumonia where the pneumonia panel was used in addition to current standard of care diagnostic methods, together with abundant opportunities for optimization of antimicrobial therapy. The study was published on January 9, 2021 in the International Journal of Infectious Diseases.

Related Links:
New York University Grossman School of Medicine
BioFire Diagnostics