Evaluation of two rapid molecular test systems to establish an algorithm for fast identification of bacterial pathogens from positive blood cultures

Abstract

Fast identification of pathogens directly from positive blood cultures is of highest importance to supply an adequate therapy of bloodstream infections (BSI). There are several platforms providing molecular-based identification, detection of antimicrobial resistance genes, or even a full antimicrobial susceptibility testing (AST). Two of such test systems allowing rapid diagnostics were assessed in this study: The Biofire FilmArray® and the Genmark ePlex®, both fully automated test system with a minimum of hands-on time. Overall 137 BSI episodes were included in our study and compared to conventional culture-based reference methods. The FilmArray® is using one catridge including a panel for the most common bacterial and fungal BSI pathogens as well as selected resistance markers. The ePlex® offers three different cartridges for detection of Gram-positives, Gram-negatives, and fungi resulting in a broader panel including also rare pathogens, putative contaminants, and more genetic resistance markers. The FilmArray® and ePlex® were evaluated for all 137 BSI episodes with FilmArray® detecting 119 and ePlex® detecting 128 of these. For targets on the respective panel of the system, the FilmArray® generated a sensitivity of 98.9% with 100% specificity on Gram-positive isolates. The ePlex® system generated a sensitivity of 94.7% and a specificity of 90.7% on Gram-positive isolates. In each case, the two systems performed with 100% sensitivity and specificity for the detection of Gram-negative specimens covered by each panel. In summary, both evaluated test systems showed a satisfying overall performance for fast pathogen identification and are beneficial tools for accelerating blood culture diagnostics of sepsis patients.

Keywords: Antibiotic resistance; Biofire FilmArray®; Bloodstream infection; GenMark ePlex®; Molecular identification; Rapid identification system.

Fig. 1

Flow chart of the study design. Each patient having a first positive blood culture signal (n = 153) with a positive initial Gram-stain (Gram-positive [n = 98] or Gram-negative bacteria [n = 33] as well as fungi [n = 6]) was included in the study (in total n = 137). Samples having more than one obvious organism according to the Gram-stain (n = 1) and Gram-stainings showing no organism (n = 8) were excluded from the study. Blood cultures positive for Gram-positive, Gram-negative organisms or fungi were analyzed with the FilmArray® and the ePlex® blood culture panels. On weekdays, PCR for Staphylococcus aureus and the mecA gene was performed directly from positive blood culture bottles, based on the Gram-stain result indicating the presence of staphylococci. Results obtained from the two evaluated test systems were compared to culture- (MALDI-TOF identification and Vitek-AST) or molecular-based (in-house PCR for Sa442 and mecA or vanA/vanB respectively) reference method