Pheno Bacterial Identification and Antimicrobial Susceptibility Determination Found to Be More Rapid and as Accurate as Existing Systems


The system allows for the rapid identification of bacteria directly from positive blood cultures, and can determine the antimicrobial susceptibility of the blood-borne pathogens.

The Accelerate Pheno system (Accelerate Diagnostics) is as accurate as existing rapid identification systems, with results available in a shorter time, according to the results of a new study. In addition, the system allows for the rapid identification of bacteria directly from positive blood cultures, and can determine the antimicrobial susceptibility of the blood-borne pathogens.

“The major findings of this study are that [the Pheno system] showed excellent agreement with pathogen identification and antibiotic susceptibility testing compared with our current standard of care,” commented Jack Schneider, MD, Indiana University School of Medicine, Indianapolis, in an interview with Contagion®. “Furthermore, [the Pheno system] has the potential to significantly reduce time to pathogen identification and antibiotic susceptibility testing results for monomicrobial bloodstream infections and improve time to antibiotic de-escalation, along with time to active and optimal therapy.” Dr. Schneider presented a poster at the 2018 Annual IDWeek Conference held in San Francisco, California, October 3-7, describing the study and the results.

The company literature claims the average time to identification of bacteria from a positive blood culture to be less than 90 minutes, with antibiotic susceptibility determined in less than 7 hours. Direct loading of positive blood cultures for testing requires less than 2 minutes. How the system compared with existing rapid bacterial identification systems in real life deserved a look.

“With a background in clinical microbiology, I have always had an interest in how the implementation of novel, rapid diagnostics can potentially improve patient outcomes,” explained Dr. Schneider. At Indiana University, our Infectious Diseases department works closely with the Medical Microbiology lab, and so when the opportunity arose to evaluate an instrument that could potentially improve turn-around times for rapid susceptibilities in our sickest patients, we seized the opportunity to collaborate and determine whether it would fit well within our laboratory workflow and stewardship capabilities.”

The investigators compared the turnaround times from sample loading to the acquisition of results for pathogen identification and antimicrobial susceptibility of the Pheno system to the timing for the current standard methods for bacterial identification. Samples testing positive on the BACTEC FX system were analyzed to identify pathogens using the Pheno and Verigene systems and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). A secondary aim was to determine whether the Pheno system could result in faster implementation of targeted and best-dose antibiotic therapy in a hospital.

The mean time to bacterial identification was 21 hours for MALDI-TOF MS, 4.5 hours for the Verigene system, and 3.7 hours for the Pheno system. The mean time to determine antibiotic susceptibility was 36 hours for the VITEK system and 9 hours for the Pheno system.

At the time when the blood-borne pathogens were identified, 39% of the 110 patients were not on active therapy. Of these, 29 were subsequently put on active therapy within a mean of 21 hours (range, 9.3 hours-5.6 days). Had the Pheno system been in place, theoretically, 28 additional patients (25%) could have commenced active therapy sooner. Treatment was optimized for 65 (59%) patients within a mean of 1.3 days (range, 9.3 hours-5.6 days). Of these 65 patients, treatment could have been optimized sooner for 51 had the Pheno system been in place, according to the study authors.

“Given that mortality increases with each hour of delayed treatment, early recognition of sepsis and initiation of targeted antibiotic therapy for patients with gram-negative rod bacteremia is crucial for optimal outcomes. Moreover, antimicrobial resistance in gram-negative rods is known to be complex. This results in limited therapeutic options, which further increases the risk of morbidity and prolonged hospitalization, as well as mortality. Thus, there is a critical need for rapid and reliable diagnostics that facilitate the timely selection of appropriate antimicrobials,” said Dr. Schneider.

The samples from the 110 patients included 13 samples that were multidrug-resistant. Escherichia coli predominated (51% of total cases, 30% of pediatric cases, and 58% of adult cases), followed by Klebsiella spp. (24%, 37%, and 19%, respectively) and Enterobacter spp. (10%, 22%, and 6%), with other bacterial pathogens detected less frequently.

“This technology has proven to be a useful tool to provide rapid and reliable identification and antibiotic susceptibility test results, but questions remain regarding its potential clinical impact. Unlike other rapid diagnostics, [the Pheno system] provides phenotypic antibiotic susceptibility results, including minimum inhibitory concentration, a format familiar to clinicians, potentially allowing for antibiotic de-escalation independent of an active stewardship intervention,” said Dr. Schneider.

The study was funded by Indiana University Medical Microbiology Laboratory. Accelerate Diagnostics, Inc, provided the Accelerate Pheno system modules and half of the kits/reagents used in the study, but did not participate in study design, data collection, or data interpretation.


Jack Schneider, MD: Accelerate Diagnostics: investigator, kits and data management, and Research support.


Poster Session: Diagnostics: Bacteria and Mycobacteria

Jack Schneider, MD

Indiana University School of Medicine

1986. Rapid Identification and Antimicrobial Susceptibility Testing Utilizing the Accelerate Pheno System for Gram-Negative Bloodstream Infections and its Potential Clinical Impact

Brian Hoyle, PhD, is a medical and science writer and editor from Halifax, Nova Scotia, Canada. He has been a full-time freelance writer/editor for over 15 years. Prior to that, he was a research microbiologist and lab manager of a provincial government water testing lab. He can be reached at

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