Syndromic Testing for Infectious Diseases, Part 4: Multiplex Panels for Positive Blood Culture Bottles

Expires January 2021



    Image of Robin Patel, M.D.Presenter

    Robin Patel, M.D., is the Division Chair of Clinical Microbiology in the Department of Laboratory Medicine and Pathology in Rochester, Minnesota. She holds the academic rank of Professor of Medicine and Microbiology.


    Contact us:


    Transcript and References


    Hi, I’m Matt Binnicker, the Director of Clinical Virology and Vice Chair of Practice in the Department of Laboratory Medicine and Pathology at Mayo Clinic. Did you know that bloodstream infections, caused by bacteria such as E. coli and Staphylococcus aureus, remain one of the most significant contributors to morbidity and mortality worldwide? So being able to quickly identify the cause of a bloodstream infection, and use that information to tailor antibiotic therapy is important in managing patients with these infections. In this month’s Hot Topic, my colleague, Dr. Robin Patel, will give the final presentation in a 4 part series on the use of syndromic molecular panels in the diagnosis of infectious diseases. Specifically, she’ll discuss how use of these multiplex tests may reduce the turnaround time for identifying the cause of bloodstream infections, and how this might impact antibiotic stewardship and patient outcomes. I hope you enjoy this month’s Hot Topic, and I want to personally thank you for allowing Mayo Clinic the opportunity to be a partner in your patients’ healthcare.

    Thank you for that introduction, Dr. Binnicker.


    My disclosures are shown on this slide.

    Utilization Management

    As you view this presentation, consider the following important points regarding testing:

    • How is the test going to be used in your practice?
    • When should the test be used?
    • How will results impact patient management?


    Bacteremia is a major cause of morbidity and mortality.

    In patients with septic shock, delays in administration of active antimicrobial therapy are associated with increased mortality.

    Early administration of active “empiric” antimicrobial treatment may, however, be compromised by antibacterial drug resistance.

    Conventional Blood Culture Practices

    Though the introduction of automated, continuous monitoring blood-culture systems has improved the diagnosis of bacteremia, there remain delays in identification of pathogens and antimicrobial susceptibility testing and in the designation of contaminants. This is because all that is typically available when a bottle signals “positive” is a Gram stain, with identification and susceptibility testing not occurring until after subcultures regrow the organism. This can impact patient-management decisions, contribute to morbidity and mortality, and potentially lead to adverse outcomes, such as Clostridium difficile-associated diarrhea and selection of antibacterial resistance.

    There are now three FDA-approved/cleared multiplex assays that simultaneously detect a number of microorganisms, as well as select resistance genes, from positive blood-culture bottles: 1. the FilmArray Blood Culture Identification (or BCID) panel from BioFire Diagnostics, which has been available since 2013, 2. the Verigene Gram-Positive Blood Culture Test (or BC-GP) from Luminex, which has been available since 2012, and 3. the Gram-Negative Blood Culture Test (or BC-GN) also from Luminex, which has been available since 2014.

    The BCID is a closed multiplex PCR system that offers automated sample preparation, amplification, detection, and analysis of 27 targets. It requires about two minutes of hands-on time to add sample from a positive blood-culture bottle to sample buffer in a single pouch, which is then loaded onto the FilmArray system. Test turnaround time is approximately one hour.

    The BC-GP and BC-GN panels use the Verigene System consisting of two components: 1. the Verigene Processor SP, which provides automated sample preparation and detection of bacterial DNA in a microarray format using gold nanoparticle probe-based technology, and 2. the Verigene Reader, which generates results based on light scatter analysis from microarray spots. The test cartridge, sample from the positive blood-culture bottle, and test consumables are loaded into the processor for sample preparation and processing. The slide from the test cartridge is then placed in the Verigene Reader to yield results. The test has a hands-on time of about 5 minutes with a run time of less than 2.5 hours.

    FilmArray® Blood Culture Identification Panel (BioFire)

    These tests are largely “add-on” tests and are quite expensive. Therefore, their value needed to be assessed. Most studies evaluating the impact of these tests have been pre- and post-intervention studies; in other words, they were studies using historical controls. Results of such studies can be confounded by changes in practice occurring over time, aside from the test itself. To overcome this limitation, our group performed a randomized controlled clinical trial evaluating the clinical impact of BCID testing of positive blood cultures along with simultaneous antimicrobial stewardship guidance.

    Randomized Controlled Clinical Trial at Mayo Clinic, 2013–2014

    In this clinical trial, 617 patients were randomized to one of three arms: 1. standard blood culture processing or our control arm, which included organism identification using MALDI-TOF mass spectrometry, 2. the BCID test reported with templated comments, or 3. the BCID test reported with templated comments and real-time audit with feedback by an antimicrobial stewardship team.

    Antibacterial Resistance Leadership Group

    The study was performed at Mayo Clinic in Rochester, Minnesota, and was supported by the Antibacterial Resistance Leadership Group of the National Institute of Allergy and Infectious Diseases of the National Institutes of Health.

    Clinical Outcomes

    There was no effect on lengths of stay, mortality, 30-day readmissions with the same organism, toxicity or adverse drug reactions, times to blood-culture clearance, development of Clostridium difficile-associated diarrhea, or acquisition of drug-resistant organisms among the study groups.

    Comparison of Time to Identification, Susceptibility Results, Antibiotic Modifications

    However, antibiotic escalation occurred sooner in both BCID groups compared to the control group, and time to de-escalation of appropriate antibiotics was notably shortest in the BCID group with concomitant antimicrobial stewardship intervention.


    Molecular panels for testing positive blood-culture bottles have several limitations. They are largely “add-on” tests because conventional subcultures and antimicrobial susceptibility testing are still required, although re-identification of isolated colonies may be avoided if the colony morphology in question is consistent with the molecularly-detected organism. To realize maximum benefits, these assays should be performed 24/7, adding logistical hurdles for both the laboratory and the stewardship system. In addition, the available panels do not cover all causes of bloodstream infection and may not be capable of identifying all pathogens in mixed infections, even if the organisms are included in the panel. False-positive results may occur. In our clinical practice, we have observed that the BCID panel may detect organisms not visualized on Gram stain or recovered in culture in 1.7% of positive BD BACTEC blood-culture bottles, with Candida parapsilosis and Proteus species being the most commonly involved organisms. The presence of nucleic acid from non-viable organisms in blood-culture bottles could potentially explain this. It is therefore important to correlate the results of these panels with Gram stain. Additionally, rare instances of species-level misidentification have been reported. For example, the Verigene BC-GP assay misidentified three of eight Streptococcus mitis as Streptococcus pneumoniae in one study. Such discrepancies may be assay-specific. While the Verigene assays offer customized ordering of different panels based on the Gram stain, this option is not available with the BCID panel. Lastly, a narrow spectrum of genes associated with drug resistance in Gram-negative bacilli is included in these panels, especially in the case of the BCID panels, and therefore, their ability to predict susceptibility of Gram-negative bacilli is imperfect.


    Overall, these assays offer minimal hands-on time and sample preparation, and they are highly automated. They have a rapid turnaround time, enabling identification of select pathogens within one to three hours, depending on the platform, theoretically allowing for early optimization of antimicrobial therapy, as well as implementation of appropriate infection prevention and control measures. In order to enable rapid escalation or de-escalation of antimicrobial therapy, results should be reported to providers as rapidly and directly as possible and should also ideally be communicated to an expert in antimicrobial stewardship who can work with providers to optimize therapy.


    1. Ramanan P, Bryson A, Binnicker M, et al. Syndromic panel-based testing in clinical microbiology. Clin Microbiol Rev 2018 Jan 31(1):e00024-17.
    2. Banerjee R, Teng CB, Cunninham SA, et al. Randomized multiplex polymerase chain reaction-based blood culture identification and susceptibility testing. Clin Infect Dis 2015 Oct 1;61(7):1071-80.

    Robin Patel, M.D. (@robinpa)

    Robin Patel, M.D.

    Robin Patel, M.D., is the Division Chair of Clinical Microbiology in the Department of Laboratory Medicine and Pathology in Rochester, Minnesota. She holds the academic rank of Professor of Medicine and Microbiology.